RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780640|ref|YP_003065053.1| hypothetical protein CLIBASIA_02635 [Candidatus Liberibacter asiaticus str. psy62] (110 letters) >gnl|CDD|178835 PRK00064, recF, recombination protein F; Reviewed. Length = 361 Score = 40.9 bits (97), Expect = 7e-05 Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%) Query: 32 IEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWL 73 + ++ FR + E +E + + ++ G+NG GK++L EAI L Sbjct: 6 LSLTDFRNYEE-LDLELSPGVNVLVGENGQGKTNLLEAIYLL 46 >gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional. Length = 895 Score = 40.3 bits (94), Expect = 1e-04 Identities = 18/44 (40%), Positives = 26/44 (59%) Query: 46 IEFADHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGDSIKK 89 IEF + I+ G+NG GKSS+ +AI + + + K D IKK Sbjct: 19 IEFDTGINIITGKNGAGKSSIVDAIRFALFTDKRTEKIEDMIKK 62 >gnl|CDD|161957 TIGR00611, recf, recF protein. All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 365 Score = 38.9 bits (91), Expect = 3e-04 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 5/65 (7%) Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGDSI 87 L +E++ FR + + +E + + ++ G NG GK++L EAI +L R H S Sbjct: 2 YLSRLELTDFRNYDAV-DLELSPGVNVIVGPNGQGKTNLLEAIYYL----ALGRSHRTSR 56 Query: 88 KKRSI 92 K I Sbjct: 57 DKPLI 61 >gnl|CDD|162739 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. Length = 1179 Score = 38.9 bits (91), Expect = 3e-04 Identities = 15/41 (36%), Positives = 25/41 (60%) Query: 32 IEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEW 72 +E++ F+ F + I F +T + G NG GKS++ +AI W Sbjct: 5 LELAGFKSFADPTTINFDKGITGIVGPNGCGKSNIVDAIRW 45 >gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 1042 Score = 38.8 bits (90), Expect = 3e-04 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 2/76 (2%) Query: 28 KLLDIEISHFRGFTEIQKIEFA--DHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGD 85 K L + + +F + I+F + ++ G+ G GK++L +AI + YG RR Sbjct: 2 KPLRLTLKNFGSYKGTHTIDFTALGPIFLICGKTGAGKTTLLDAITYALYGKLPRRSEVI 61 Query: 86 SIKKRSIKTPMPMCMA 101 P A Sbjct: 62 RSLNSLYAAPSEAAFA 77 >gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional. Length = 880 Score = 36.6 bits (85), Expect = 0.001 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 3/62 (4%) Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRRKHGDSI 87 K+ +++I +FR + +EF D + ++ GQNG GKSS+ EAI Y + G + Sbjct: 2 KIEELKIKNFRSH-KSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWGHGSKPKG--L 58 Query: 88 KK 89 KK Sbjct: 59 KK 60 >gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional. Length = 880 Score = 36.2 bits (84), Expect = 0.002 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%) Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76 + + + +F+ + + + D +T+++G NG GKSSL EA + YG Sbjct: 2 RFDRVRLENFKCYADAD-LRLEDGVTVIHGVNGSGKSSLLEACFFALYG 49 >gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. Length = 1164 Score = 33.1 bits (76), Expect = 0.015 Identities = 17/43 (39%), Positives = 29/43 (67%), Gaps = 2/43 (4%) Query: 32 IEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLF 74 IE+ +F+ F + + I F+ T+++G NG GKS++ +AI LF Sbjct: 5 IELENFKSFGKKKVIPFSKGFTVISGPNGSGKSNIGDAI--LF 45 >gnl|CDD|161971 TIGR00634, recN, DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair. Length = 563 Score = 31.6 bits (72), Expect = 0.044 Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%) Query: 29 LLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLF 74 L ++ I++F + +EF LT++ G+ G GKS + +A+ L Sbjct: 2 LTELRINNF-ALIRVLTVEFERGLTVLTGETGAGKSMIIDALSLLG 46 >gnl|CDD|129694 TIGR00606, rad50, rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 1311 Score = 29.6 bits (66), Expect = 0.16 Identities = 13/35 (37%), Positives = 23/35 (65%) Query: 42 EIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76 + Q I+F LTI+ G NG GK+++ E ++++ G Sbjct: 20 DKQIIDFFSPLTILVGPNGAGKTTIIECLKYICTG 54 >gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed. Length = 298 Score = 29.8 bits (68), Expect = 0.16 Identities = 10/24 (41%), Positives = 16/24 (66%) Query: 48 FADHLTIVNGQNGYGKSSLSEAIE 71 A +T++ GQ+G GKS+L A+ Sbjct: 162 LAGKVTVLAGQSGVGKSTLLNALA 185 >gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional. Length = 349 Score = 29.8 bits (67), Expect = 0.17 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%) Query: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIE 71 +LL + ++R + F +T V G+N GK++L EAI Sbjct: 2 RLLSLRQLNYRNLA-PPTLAFPPGVTAVVGENAAGKTNLLEAIY 44 >gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed. Length = 352 Score = 29.6 bits (67), Expect = 0.20 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 10/66 (15%) Query: 10 CACLSKS-LTSYYARKLI--------FKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNG 60 CL+K+ L S ++ ++ L I + G + + + + +T+V G +G Sbjct: 124 VLCLNKADLVSPTEQQQWQDRLQQWGYQPLFISVETGIGLEALLE-QLRNKITVVAGPSG 182 Query: 61 YGKSSL 66 GKSSL Sbjct: 183 VGKSSL 188 >gnl|CDD|183406 PRK12288, PRK12288, GTPase RsgA; Reviewed. Length = 347 Score = 29.0 bits (66), Expect = 0.27 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%) Query: 23 RKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSL 66 R + +++L + G E++ ++I GQ+G GKSSL Sbjct: 179 RNIGYRVLMVSSHTGEGLEELEA-ALTGRISIFVGQSGVGKSSL 221 >gnl|CDD|161735 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). Length = 245 Score = 28.1 bits (63), Expect = 0.54 Identities = 9/24 (37%), Positives = 15/24 (62%) Query: 47 EFADHLTIVNGQNGYGKSSLSEAI 70 + +++ GQ+G GKSSL A+ Sbjct: 117 ALQNRISVFAGQSGVGKSSLINAL 140 >gnl|CDD|150128 pfam09352, DUF1994, Domain of unknown function (DUF1994). This family of proteins are functionally uncharacterized. Length = 162 Score = 27.7 bits (62), Expect = 0.73 Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 15/85 (17%) Query: 3 RLRKKNTCACLSKSLTSYYARKLIFKLLDIEISHF-----------RGFTEIQKIEFA-- 49 + CA S +L Y K I ++I H +T+ Q+ FA Sbjct: 48 TFKTGKRCAVASGTLHDPYTGKTITTAAAVDIDHVVPLAEAWDSGASSWTDRQRERFAND 107 Query: 50 -DHLTIVNGQNGYGKSSLSEAIEWL 73 +L V+G K + EWL Sbjct: 108 PANLLAVDGSANRSKGD-KDPAEWL 131 >gnl|CDD|182751 PRK10811, rne, ribonuclease E; Reviewed. Length = 1068 Score = 26.9 bits (60), Expect = 1.1 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 7/39 (17%) Query: 60 GYGKSSLSEAIEW-LFYGYTQRRKHGDSIKKRSIKTPMP 97 G GKS+ EA++W L + R KH ++IKK + P P Sbjct: 172 GVGKSA--EALQWDLSF----RLKHWEAIKKAAESRPAP 204 >gnl|CDD|177394 PHA02562, 46, endonuclease subunit; Provisional. Length = 562 Score = 26.9 bits (60), Expect = 1.2 Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 2/37 (5%) Query: 40 FTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76 EIQ + T++ G+NG GKS++ EA+ + +G Sbjct: 19 PIEIQLDKVKK--TLITGKNGAGKSTMLEALTFALFG 53 >gnl|CDD|184126 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA; Provisional. Length = 207 Score = 26.4 bits (59), Expect = 1.6 Identities = 7/19 (36%), Positives = 11/19 (57%) Query: 48 FADHLTIVNGQNGYGKSSL 66 A ++ G NG GK++L Sbjct: 26 AAGEALVLTGPNGSGKTTL 44 >gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD family. Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown. Length = 552 Score = 26.4 bits (59), Expect = 1.8 Identities = 21/66 (31%), Positives = 25/66 (37%), Gaps = 25/66 (37%) Query: 1 MTRLRKKNTCACLSKSLTSYYARKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNG 60 M R+ K +K I K DI +S F G KI V G NG Sbjct: 7 MNRVSK------------VVPPKKEILK--DISLSFFPG----AKIG-------VLGLNG 41 Query: 61 YGKSSL 66 GKS+L Sbjct: 42 AGKSTL 47 >gnl|CDD|162972 TIGR02680, TIGR02680, conserved hypothetical protein TIGR02680. Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. Length = 1353 Score = 26.3 bits (58), Expect = 2.0 Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 1/35 (2%) Query: 44 QKIEFADHLTIVNGQNGYGKS-SLSEAIEWLFYGY 77 Q+ F D ++ G NG GKS L + +L G Sbjct: 18 QEFWFRDGRLLLRGNNGAGKSKVLELLLPFLLDGK 52 >gnl|CDD|182852 PRK10938, PRK10938, putative molybdenum transport ATP-binding protein ModF; Provisional. Length = 490 Score = 26.1 bits (58), Expect = 2.1 Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 7/29 (24%) Query: 50 DHLTIVNGQ-------NGYGKSSLSEAIE 71 LT+ G NG GKS+L+ A+ Sbjct: 22 PSLTLNAGDSWAFVGANGSGKSALARALA 50 >gnl|CDD|152563 pfam12128, DUF3584, Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. There are two conserved sequence motifs: GKT and YLP. Length = 1192 Score = 25.8 bits (57), Expect = 2.3 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%) Query: 35 SHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYG 76 SH G + +++ H T + G N GK++L I LFYG Sbjct: 5 SHLPGV--VNELDLDGH-TNICGTNAAGKTTLQRLIP-LFYG 42 >gnl|CDD|163250 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding protein UrtE. Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Length = 230 Score = 25.6 bits (57), Expect = 2.7 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 13/56 (23%) Query: 15 KSLTSYYARKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAI 70 +L YY + I + + +E+ +T V G+NG GK++L + + Sbjct: 4 SNLNVYYGQSHILRGVSLEVP-------------KGEVTCVLGRNGVGKTTLLKTL 46 >gnl|CDD|162608 TIGR01928, menC_lowGC/arch, o-succinylbenzoic acid (OSB) synthetase. This model describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Included in this model are low GC gram positive bacteria and archaea. Also included in the seed and in the model are enzymes with the com-name of N-acylamino acid racemase (or the more general term, racemase / racemase family), which refers to the enzyme's industrial application as racemases, and not to its biological function as o-succinylbenzoic acid synthetase. Length = 324 Score = 25.6 bits (56), Expect = 2.8 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 8/57 (14%) Query: 1 MTRLRKKN--TCACLSKSLTSYY-ARKLI----FKLLDIEISHFRGFTEIQK-IEFA 49 M K T CL +S+TS AR LI K+++I+ G TE+QK IE Sbjct: 214 MLDELAKGTITPICLDESITSLDDARNLIELGNVKVINIKPGRLGGLTEVQKAIETC 270 >gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional. Length = 263 Score = 25.5 bits (56), Expect = 3.1 Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%) Query: 39 GFTEIQKIEFADHLTIVNG-QNGYGKSSLSEAI 70 G T+ +E+A VN GY ++ ++E+I Sbjct: 164 GLTKSLAVEYAQSGIRVNAICPGYVRTPMAESI 196 >gnl|CDD|184195 PRK13635, cbiO, cobalt transporter ATP-binding subunit; Provisional. Length = 279 Score = 25.4 bits (56), Expect = 3.1 Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%) Query: 52 LTIVNGQNGYGKSSLSEAIEWLF 74 + IV G NG GKS+L++ + L Sbjct: 36 VAIV-GHNGSGKSTLAKLLNGLL 57 >gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional. Length = 444 Score = 25.2 bits (55), Expect = 3.6 Identities = 9/17 (52%), Positives = 14/17 (82%) Query: 54 IVNGQNGYGKSSLSEAI 70 ++NGQ+G GK L++AI Sbjct: 161 LINGQSGTGKEILAQAI 177 >gnl|CDD|162636 TIGR01978, sufC, FeS assembly ATPase SufC. SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA. Length = 243 Score = 25.3 bits (56), Expect = 4.0 Identities = 9/17 (52%), Positives = 12/17 (70%) Query: 54 IVNGQNGYGKSSLSEAI 70 + G NG GKS+LS+ I Sbjct: 30 AIMGPNGSGKSTLSKTI 46 >gnl|CDD|184717 PRK14508, PRK14508, 4-alpha-glucanotransferase; Provisional. Length = 497 Score = 24.8 bits (55), Expect = 4.8 Identities = 11/15 (73%), Positives = 11/15 (73%), Gaps = 1/15 (6%) Query: 27 FKLLDI-EISHFRGF 40 FKL DI I HFRGF Sbjct: 288 FKLYDIVRIDHFRGF 302 >gnl|CDD|162633 TIGR01973, NuoG, NADH-quinone oxidoreductase, chain G. This model represents the G subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes related subunits from formate dehydrogenase complexes. Length = 603 Score = 25.0 bits (55), Expect = 4.9 Identities = 13/41 (31%), Positives = 16/41 (39%), Gaps = 12/41 (29%) Query: 74 FYGYTQRRKHGDSIKKRS---------IKTPMPMCMAVPRC 105 YG + R KKR+ IKT M C+ RC Sbjct: 113 MYGSDRSRFRE---KKRTVENKYLGPLIKTEMTRCIHCTRC 150 >gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated. Length = 234 Score = 24.9 bits (55), Expect = 5.0 Identities = 8/21 (38%), Positives = 13/21 (61%) Query: 52 LTIVNGQNGYGKSSLSEAIEW 72 L ++ G +G GKS LS+ + Sbjct: 27 LILIEGDHGTGKSVLSQQFVY 47 >gnl|CDD|163179 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. Length = 650 Score = 24.6 bits (54), Expect = 5.0 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 6/57 (10%) Query: 25 LIFKLLDIEISHFRGFTEIQKIEFA----DHLTIVNGQNGYGKSSLSEAIEWLFYGY 77 +I L +E +F + Q + + + ++ G NG GK++L +AI+ YG Sbjct: 1 MIILQLTLE--NFGPYRGRQTFDLSPSSPKPIILIGGLNGAGKTTLLDAIQLALYGK 55 >gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR; Provisional. Length = 638 Score = 24.6 bits (54), Expect = 5.3 Identities = 7/17 (41%), Positives = 13/17 (76%) Query: 54 IVNGQNGYGKSSLSEAI 70 ++ G+ G GK+ L++AI Sbjct: 352 LLCGEEGVGKALLAQAI 368 >gnl|CDD|183324 PRK11819, PRK11819, putative ABC transporter ATP-binding protein; Reviewed. Length = 556 Score = 24.7 bits (55), Expect = 5.6 Identities = 21/66 (31%), Positives = 25/66 (37%), Gaps = 25/66 (37%) Query: 1 MTRLRKKNTCACLSKSLTSYYARKLIFKLLDIEISHFRGFTEIQKIEFADHLTIVNGQNG 60 M R+ K +K I K DI +S F G KI V G NG Sbjct: 9 MNRVSK------------VVPPKKQILK--DISLSFFPG----AKIG-------VLGLNG 43 Query: 61 YGKSSL 66 GKS+L Sbjct: 44 AGKSTL 49 >gnl|CDD|184202 PRK13642, cbiO, cobalt transporter ATP-binding subunit; Provisional. Length = 277 Score = 24.7 bits (53), Expect = 5.9 Identities = 10/18 (55%), Positives = 13/18 (72%) Query: 57 GQNGYGKSSLSEAIEWLF 74 GQNG GKS+ + I+ LF Sbjct: 40 GQNGSGKSTTARLIDGLF 57 >gnl|CDD|130996 TIGR01941, nqrF, NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit. This model represents the NqrF subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump. Length = 405 Score = 24.4 bits (53), Expect = 6.2 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 6/51 (11%) Query: 6 KKNTCACLSKSLTSYYARKLIFKLLDIEISHFR--GFTEIQ----KIEFAD 50 KK C +S + + ++L+ KL D E F+ G+ +I+ +++AD Sbjct: 128 KKWECEVISNDNVATFIKELVLKLPDGESVPFKAGGYIQIEAPPHVVKYAD 178 >gnl|CDD|184128 PRK13541, PRK13541, cytochrome c biogenesis protein CcmA; Provisional. Length = 195 Score = 24.4 bits (53), Expect = 6.6 Identities = 10/19 (52%), Positives = 12/19 (63%) Query: 52 LTIVNGQNGYGKSSLSEAI 70 +T + G NG GKSSL I Sbjct: 28 ITYIKGANGCGKSSLLRMI 46 >gnl|CDD|182970 PRK11111, PRK11111, hypothetical protein; Provisional. Length = 214 Score = 24.1 bits (53), Expect = 7.4 Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 3/36 (8%) Query: 6 KKNTCACLSKS---LTSYYARKLIFKLLDIEISHFR 38 K N A LS + L S + I L I I FR Sbjct: 44 KTNLTANLSVAIILLISLFLGDFILNLFGISIDSFR 79 >gnl|CDD|150482 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members of this family include various bacterial predicted ABC class ATPases. Length = 447 Score = 24.1 bits (53), Expect = 8.6 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 52 LTIVNGQNGYGKSSLSEAIE 71 +T++ G +GKS+L EA+E Sbjct: 245 ITLIVGGGYHGKSTLLEALE 264 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.324 0.136 0.413 Gapped Lambda K H 0.267 0.0771 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,729,884 Number of extensions: 92060 Number of successful extensions: 300 Number of sequences better than 10.0: 1 Number of HSP's gapped: 300 Number of HSP's successfully gapped: 47 Length of query: 110 Length of database: 5,994,473 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,352,265 Effective search space: 147977010 Effective search space used: 147977010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.0 bits)