-- dump date   	20120504_151721
-- class       	Genbank::misc_feature
-- table       	misc_feature_note
-- id	note
1107880000001	potential frameshift: common BLAST hit: gi|339491607|ref|YP_004706112.1| adenosylmethionine-8-amino-7-oxononanoate aminotransferase
1107880000002	potential frameshift: common BLAST hit: gi|116617540|ref|YP_817911.1| major facilitator superfamily permease
1107880000003	potential frameshift: common BLAST hit: gi|116617954|ref|YP_818325.1| AraC family transcriptional regulator
1107880000004	potential frameshift: common BLAST hit: gi|116618010|ref|YP_818381.1| trehalose PTS trehalose component IIBC
1107880000005	potential frameshift: common BLAST hit: gi|116618064|ref|YP_818435.1| DNA-binding response regulator
1107880000006	potential frameshift: common BLAST hit: gi|289551807|ref|YP_003472711.1| LacI family transcriptinal regulator
1107880000007	potential frameshift: common BLAST hit: gi|116618172|ref|YP_818543.1| transposase
1107880000008	potential frameshift: common BLAST hit: gi|170017259|ref|YP_001728178.1| Type IC restriction subunit
1107880000009	potential frameshift: common BLAST hit: gi|116618238|ref|YP_818609.1| cytidine deaminase
1107880000010	potential frameshift: common BLAST hit: gi|296110935|ref|YP_003621316.1| major facilitator family transporter
1107880000011	potential frameshift: common BLAST hit: gi|116618331|ref|YP_818702.1| major facilitator superfamily permease
1107880000012	potential frameshift: common BLAST hit: gi|28377765|ref|NP_784657.1| site-specific DNA-methyltransferase (adenine-specific), HsdM
1107880000013	potential frameshift: common BLAST hit: gi|116619095|ref|YP_819466.1| high-affinity nickel permease
1107880000014	Helix-turn-helix domains; Region: HTH; cl00088
1107880000015	Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768
1107880000016	catalytic residues [active]
1107880000017	catalytic nucleophile [active]
1107880000018	Presynaptic Site I dimer interface [polypeptide binding]; other site
1107880000019	Synaptic Antiparallel dimer interface [polypeptide binding]; other site
1107880000020	Synaptic Flat tetramer interface [polypeptide binding]; other site
1107880000021	Synaptic Site I dimer interface [polypeptide binding]; other site
1107880000022	DNA binding site [nucleotide binding]
1107880000023	CrcB-like protein; Region: CRCB; cl09114
1107880000024	CrcB-like protein; Region: CRCB; cl09114
1107880000025	ClC chloride channel EriC.  This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031
1107880000026	Voltage gated chloride channel; Region: Voltage_CLC; pfam00654
1107880000027	Cl- selectivity filter; other site
1107880000028	Cl- binding residues [ion binding]; other site
1107880000029	pore gating glutamate residue; other site
1107880000030	dimer interface [polypeptide binding]; other site
1107880000031	H+/Cl- coupling transport residue; other site
1107880000032	Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357
1107880000033	Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482
1107880000034	Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999
1107880000035	Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432
1107880000036	Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432
1107880000037	Helix-turn-helix domains; Region: HTH; cl00088
1107880000038	Low molecular weight phosphatase family; Region: LMWPc; cd00115
1107880000039	Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451
1107880000040	active site
1107880000041	CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656
1107880000042	ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042
1107880000043	P-loop; other site
1107880000044	Magnesium ion binding site [ion binding]; other site
1107880000045	ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042
1107880000046	Magnesium ion binding site [ion binding]; other site
1107880000047	Domain of unknown function (DUF955); Region: DUF955; cl01076
1107880000048	multicopper oxidase; Provisional; Region: PRK10965
1107880000049	Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412
1107880000050	Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412
1107880000051	Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446
1107880000052	Helix-turn-helix domains; Region: HTH; cl00088
1107880000053	HTH-like domain; Region: HTH_21; pfam13276
1107880000054	Integrase core domain; Region: rve; cl01316
1107880000055	Integrase core domain; Region: rve_3; cl15866
1107880000056	Plasmid recombination enzyme; Region: Mob_Pre; pfam01076
1107880000057	pyridine nucleotide-disulfide oxidoreductase; Provisional; Region: PRK07251
1107880000058	Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931
1107880000059	Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070
1107880000060	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852
1107880000061	Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860
1107880000062	DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213
1107880000063	potential frameshift: common BLAST hit: gi|170016270|ref|YP_001722993.1| cation transport ATPase
1107880000064	Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371
1107880000065	metal-binding site [ion binding]
1107880000066	Ferritin-like domain; Region: Ferritin; pfam00210
1107880000067	DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043
1107880000068	dimerization interface [polypeptide binding]; other site
1107880000069	DPS ferroxidase diiron center [ion binding]; other site
1107880000070	ion pore; other site
1107880000071	cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664
1107880000072	effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038
1107880000073	ligand binding site [chemical binding]; other site
1107880000074	flexible hinge region; other site
1107880000075	helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092
1107880000076	putative switch regulator; other site
1107880000077	non-specific DNA interactions [nucleotide binding]; other site
1107880000078	DNA binding site [nucleotide binding]
1107880000079	sequence specific DNA binding site [nucleotide binding]; other site
1107880000080	putative cAMP binding site [chemical binding]; other site
1107880000081	CCC1-related family of proteins; Region: CCC1_like; cd01059
1107880000082	DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213
1107880000083	active site
1107880000084	DNA binding site [nucleotide binding]
1107880000085	Int/Topo IB signature motif; other site
1107880000086	Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424
1107880000087	ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4619
1107880000088	Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota.  The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed.  This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225
1107880000089	Walker A/P-loop; other site
1107880000090	ATP binding site [chemical binding]; other site
1107880000091	Q-loop/lid; other site
1107880000092	ABC transporter signature motif; other site
1107880000093	Walker B; other site
1107880000094	D-loop; other site
1107880000095	H-loop/switch region; other site
1107880000096	Helix-turn-helix domains; Region: HTH; cl00088
1107880000097	3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726
1107880000098	active site
1107880000099	dimer interface [polypeptide binding]; other site
1107880000100	magnesium binding site [ion binding]; other site
1107880000101	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389
1107880000102	Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033
1107880000103	putative uracil binding site [chemical binding]; other site
1107880000104	putative active site [active]
1107880000105	5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360
1107880000106	Integrase core domain; Region: rve; cl01316
1107880000107	Integrase core domain; Region: rve_3; cl15866
1107880000108	TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108
1107880000109	RelB antitoxin; Region: RelB; cl01171
1107880000110	PemK-like protein; Region: PemK; cl00995
1107880000111	This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632
1107880000112	helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344
1107880000113	Helix-turn-helix domains; Region: HTH; cl00088
1107880000114	P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099
1107880000115	Walker A/P-loop; other site
1107880000116	ATP binding site [chemical binding]; other site
1107880000117	Q-loop/lid; other site
1107880000118	AAA domain; Region: AAA_21; pfam13304
1107880000119	P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099
1107880000120	Q-loop/lid; other site
1107880000121	ABC transporter signature motif; other site
1107880000122	Walker B; other site
1107880000123	D-loop; other site
1107880000124	H-loop/switch region; other site
1107880000125	P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099
1107880000126	AAA domain; Region: AAA_21; pfam13304
1107880000127	Walker A/P-loop; other site
1107880000128	ATP binding site [chemical binding]; other site
1107880000129	Q-loop/lid; other site
1107880000130	ABC transporter signature motif; other site
1107880000131	Walker B; other site
1107880000132	D-loop; other site
1107880000133	H-loop/switch region; other site
1107880000134	TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947
1107880000135	catalytic residues [active]
1107880000136	CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385
1107880000137	Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070
1107880000138	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852
1107880000139	Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524
1107880000140	active site residue [active]
1107880000141	Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156; Region: BsYrkD-like_DUF156; cd10155
1107880000142	putative homodimer interface [polypeptide binding]; other site
1107880000143	putative homotetramer interface [polypeptide binding]; other site
1107880000144	putative metal binding site [ion binding]; other site
1107880000145	putative homodimer-homodimer interface [polypeptide binding]; other site
1107880000146	putative allosteric switch controlling residues; other site
1107880000147	Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446
1107880000148	potential frameshift: common BLAST hit: gi|308181749|ref|YP_003925877.1| GTP-binding protein LepA
1107880000149	Helix-turn-helix domains; Region: HTH; cl00088
1107880000150	biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244
1107880000151	NADH(P)-binding; Region: NAD_binding_10; pfam13460
1107880000152	NAD binding site [chemical binding]; other site
1107880000153	substrate binding site [chemical binding]; other site
1107880000154	putative active site [active]
1107880000155	TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947
1107880000156	catalytic residues [active]
1107880000157	Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768
1107880000158	catalytic residues [active]
1107880000159	catalytic nucleophile [active]
1107880000160	Presynaptic Site I dimer interface [polypeptide binding]; other site
1107880000161	Synaptic Antiparallel dimer interface [polypeptide binding]; other site
1107880000162	Synaptic Flat tetramer interface [polypeptide binding]; other site
1107880000163	Synaptic Site I dimer interface [polypeptide binding]; other site
1107880000164	DNA binding site [nucleotide binding]
1107880000165	S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl16911
1107880000166	P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099
1107880000167	ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192
1107880000168	ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042
1107880000169	Magnesium ion binding site [ion binding]; other site
1107880000170	Domain of unknown function (DUF955); Region: DUF955; cl01076
1107880000171	P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099
1107880000172	Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761
1107880000173	Replication initiation factor; Region: Rep_trans; pfam02486
1107880000174	Conjugative transposon protein TcpC; Region: TpcC; pfam12642
1107880000175	TcpE family; Region: TcpE; pfam12648
1107880000176	Antirestriction protein (ArdA); Region: ArdA; cl01953
1107880000177	AAA-like domain; Region: AAA_10; pfam12846
1107880000178	TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503
1107880000179	MAEBL; Provisional; Region: PTZ00121
1107880000180	TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947
1107880000181	catalytic residues [active]
1107880000182	thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292
1107880000183	Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931
1107880000184	Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070
1107880000185	TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947
1107880000186	catalytic residues [active]
1107880000187	TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947
1107880000188	catalytic residues [active]
1107880000189	TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947
1107880000190	catalytic residues [active]
1107880000191	Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090
1107880000192	dimerization interface [polypeptide binding]; other site
1107880000193	putative DNA binding site [nucleotide binding]; other site
1107880000194	putative Zn2+ binding site [ion binding]; other site
1107880000195	Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158
1107880000196	active site residue [active]
1107880000197	Predicted helicase [General function prediction only]; Region: COG4889
1107880000198	Restriction endonuclease; Region: Mrr_cat; cl00516
1107880000199	P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099
1107880000200	P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099
1107880000201	Protein involved in initiation of plasmid replication [DNA replication, recombination, and repair]; Region: COG5527
1107880000202	Initiator Replication protein; Region: Rep_3; cl03080
1107880000203	Lactococcus lactis RepB C-terminus; Region: L_lactis_RepB_C; pfam06430
1107880000204	Plasmid recombination enzyme; Region: Mob_Pre; pfam01076
1107880000205	N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357
1107880000206	sucrose-6-phosphate hydrolase; Region: scrB_fam; TIGR01322
1107880000207	Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996
1107880000208	substrate binding [chemical binding]; other site
1107880000209	active site
1107880000210	Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244
1107880000211	galactoside permease; Reviewed; Region: lacY; PRK09528
1107880000212	The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174
1107880000213	putative substrate translocation pore; other site
1107880000214	Transcriptional regulators [Transcription]; Region: PurR; COG1609
1107880000215	Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392
1107880000216	DNA binding site [nucleotide binding]
1107880000217	domain linker motif; other site
1107880000218	Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; Region: PBP1_Qymf_like; cd06291
1107880000219	dimerization interface [polypeptide binding]; other site
1107880000220	ligand binding site [chemical binding]; other site
1107880000221	sodium binding site [ion binding]; other site
1107880000222	Transposase; Region: DDE_Tnp_ISL3; pfam01610
1107880000223	Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249
1107880000224	Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070
1107880000225	Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761
1107880000226	DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024
1107880000227	catalytic residues [active]