RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780766|ref|YP_003065179.1| recombination protein F [Candidatus Liberibacter asiaticus str. psy62] (375 letters) >gnl|CDD|178835 PRK00064, recF, recombination protein F; Reviewed. Length = 361 Score = 344 bits (886), Expect = 2e-95 Identities = 124/365 (33%), Positives = 191/365 (52%), Gaps = 13/365 (3%) Query: 7 IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTR 66 + L++++FRNY L L + VG+NG GKTN+LEAI L+PGR R A ++ R Sbjct: 3 LTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIR 62 Query: 67 IGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLV 126 G+ + RVE + ++++ + R VR IN R + EL L + Sbjct: 63 FGAEAAV-IHGRVEKGGRELPLGLEIDKKGGRKVR---INGEPQRKLAELAGLLNVVLFT 118 Query: 127 PSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCSSI 186 P R+ G ERRRFLDR++F I+P + + +ER ++ RN LL + D +W Sbjct: 119 PEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQRNALLKQA--DYAWLDVW 176 Query: 187 EAQMAELGVKINIARVEMINALSSLIMEYVQKEN--FPHIKLSLTGFLDGKFDQSFCALK 244 + Q+AELG I AR+E + L+ L + Q+ + F LS + + ++ Sbjct: 177 DEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSV----EDDAEKIE 232 Query: 245 EEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHA 304 E+ + L R+ D RTL+GPHR DL + GSTG+QK++L+ + LA A Sbjct: 233 EDLLEALAKNRERDRARGRTLVGPHRDDLRF-RINGLPAADFGSTGQQKLLLLALKLAEA 291 Query: 305 RLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDSLNETAKF 364 L+ TG APILLLD++++ LD+ +R AL + +G+Q+F+T TD L E AK Sbjct: 292 ELLKEETGEAPILLLDDVASELDDGRRAALLERLKGLGAQVFITTTDLEDLADLLENAKI 351 Query: 365 MRISN 369 + Sbjct: 352 FHVEQ 356 >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 = 151 bits (384), Expect = 2e-37 Identities = 97/350 (27%), Positives = 165/350 (47%), Gaps = 13/350 (3%) Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVT 65 + L +++FRNY ++ L + VG NG GKTN+LEAI +L+ GR R + + Sbjct: 2 YLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLI 61 Query: 66 RIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWL 125 R G+ +F RV + +++I LE + + ++N + +L L + Sbjct: 62 RFGAEAFV-IEGRVSKGDR--EVTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLF 118 Query: 126 VPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEG---YFDSSW 182 P + G RRRFLD +F ++P + D++R+++ RN L + Y D + Sbjct: 119 APEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLKQRNAALKQAQRQYGDRTT 178 Query: 183 CSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCA 242 ++Q+AELG K++ R E I L + Q SL+ F G+ Sbjct: 179 LEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQ--LLLPELESLSLFYRGELW----D 232 Query: 243 LKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLA 302 + +YA+ L + D TL+GPHR DL + S G+ + + + + LA Sbjct: 233 KETDYAEALARNFERDLERGYTLVGPHRDDLRF-RLNGLPVEDFASQGQLRSLALALRLA 291 Query: 303 HARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDK 352 L+ G PILLLD++++ LD+ +R L ++ +G Q+F+T Sbjct: 292 EGELLREEGGEYPILLLDDVASELDDQRRRLLAELLQSLGVQVFVTAISL 341 >gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional. Length = 349 Score = 107 bits (268), Expect = 6e-24 Identities = 94/339 (27%), Positives = 152/339 (44%), Gaps = 24/339 (7%) Query: 15 FRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFS 74 +RN A L F T VG+N GKTN+LEAI +L+ AD+ R G + Sbjct: 11 YRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAI-YLALTGELPNGRLADLVRFGEGEAW- 68 Query: 75 TFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFS 134 A VE GL+ +LE R L+++ V + + EL + + P + Sbjct: 69 VHAEVETGGGLS----RLEVGLGPGRRELKLDGVRVSL-RELARLPGAVLIRPEDLELVL 123 Query: 135 GLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCSSI-EAQMAEL 193 G RR +LDR++ + R+ + +ER ++ RN L G W + + ++ +L Sbjct: 124 GPPEGRRAYLDRLLSRLSARYAALLSAYERAVQQRNAALKSG---GGWGLHVWDDELVKL 180 Query: 194 GVKINIARVEMINALSSLIME-YVQKENFPHIKLSLTGFLDGKFDQSFCALKEEYAKKLF 252 G +I R + LS L E Y + + ++L L+ E Y L Sbjct: 181 GDEIMALRRRALTRLSELAREAYAELGSRKPLRLELSESTAP----------EGYLAALE 230 Query: 253 DGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNTTG 312 R + T++GPHR DL++ + + S GE + V + + LA RL+ G Sbjct: 231 ARRAEELARGATVVGPHRDDLVLTLEGRPAH-RYASRGEARTVALALRLAEHRLLWEHFG 289 Query: 313 FAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTD 351 AP+LL+D+ +A LD +R AL + + Q + GT+ Sbjct: 290 EAPVLLVDDFTAELDPRRRGALLALAASL-PQAIVAGTE 327 >gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional. Length = 880 Score = 41.6 bits (98), Expect = 3e-04 Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 3/68 (4%) Query: 5 IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAIS---FLSPGRGFRRASY 61 +KI+ L I FR++ S + FD + +G NG GK++ILEAI + G + Sbjct: 1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWGHGSKPKGLKK 60 Query: 62 ADVTRIGS 69 D TRIG Sbjct: 61 DDFTRIGG 68 >gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148 Score = 35.8 bits (82), Expect = 0.018 Identities = 24/142 (16%), Positives = 42/142 (29%), Gaps = 7/142 (4%) Query: 28 QHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGMEGLAD 87 + + VG G GKT + A++ G Y D I + G + + Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPG-GGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61 Query: 88 ISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSMERRRFLDRM 147 R ++ DV+I +DE+ L + L + + + Sbjct: 62 SGELRL-RLALALARKLKPDVLI--LDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLT 118 Query: 148 VFAIDPRHRRRMIDFERLMRGR 169 V L+R R Sbjct: 119 VILT---TNDEKDLGPALLRRR 137 >gnl|CDD|177394 PHA02562, 46, endonuclease subunit; Provisional. Length = 562 Score = 34.6 bits (80), Expect = 0.039 Identities = 13/32 (40%), Positives = 20/32 (62%) Query: 26 DAQHTIFVGDNGVGKTNILEAISFLSPGRGFR 57 + T+ G NG GK+ +LEA++F G+ FR Sbjct: 26 KVKKTLITGKNGAGKSTMLEALTFALFGKPFR 57 >gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional. Length = 895 Score = 34.5 bits (79), Expect = 0.044 Identities = 15/43 (34%), Positives = 24/43 (55%) Query: 7 IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF 49 IK + + F ++ + FD I G NG GK++I++AI F Sbjct: 3 IKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRF 45 Score = 32.6 bits (74), Expect = 0.20 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 3/51 (5%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338 S GE+ V + +A A+ ++N L++DE +A LDED+R L I+ Sbjct: 803 SGGEKTAVAFALRVAVAQFLNNDKSL---LIMDEPTAFLDEDRRTNLKDII 850 >gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed. Length = 402 Score = 34.4 bits (79), Expect = 0.046 Identities = 29/95 (30%), Positives = 40/95 (42%), Gaps = 34/95 (35%) Query: 252 FDGRKMDSMSRRTLIGPHRS---------DLIVD----------YCDKAITIAHGSTGEQ 292 FD R++ M R PHRS V+ + D+ +T G GE+ Sbjct: 92 FDVRQVVEMGRT----PHRSRFDTWTETDRAAVERAMERTGVAQFADRPVTSLSG--GER 145 Query: 293 KVVLVGIFLAHARLISNTTGFAPILLLDEISAHLD 327 + VL+ LA A P+LLLDE +A LD Sbjct: 146 QRVLLARALAQA---------TPVLLLDEPTASLD 171 Score = 28.3 bits (63), Expect = 3.3 Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%) Query: 33 VGDNGVGKTNILEAIS-FLSPGRG 55 VG NG GKT +L AI+ L+P G Sbjct: 35 VGPNGAGKTTLLRAINGTLTPTAG 58 >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 = 34.3 bits (79), Expect = 0.047 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 11/98 (11%) Query: 10 LNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGS 69 L I+ F L + F+ T+ G+ G GK+ I++A+S L R A R G Sbjct: 5 LRINNFALIRVLTVEFERGLTVLTGETGAGKSMIIDALSLLGGQRA-----GASRVRSGE 59 Query: 70 PS------FFSTFARVEGMEGLADISIKLETRDDRSVR 101 F + L I ++ E D + Sbjct: 60 NRAVVEGRFTTESLDDADYPALQAIELEEEDEDGEVIL 97 >gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional. Length = 880 Score = 33.9 bits (78), Expect = 0.066 Identities = 14/44 (31%), Positives = 23/44 (52%) Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF 49 + + + F+ YA L + T+ G NG GK+++LEA F Sbjct: 2 RFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEACFF 45 >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 = 33.9 bits (78), Expect = 0.076 Identities = 29/128 (22%), Positives = 45/128 (35%), Gaps = 16/128 (12%) Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRASYA 62 +I+ N F + F T+ G NG GK+NI +AI F LS + R + Sbjct: 4 RIELENFKSFGKKK--VIPFSKGFTVISGPNGSGKSNIGDAILFALGLSSSKAMRAERLS 61 Query: 63 DVTRIGSPSFFSTFARVE--------GMEGLADISIKLETRDDRSVRCLQINDVVIR--- 111 D+ G A V ++ +L+ DD +N +R Sbjct: 62 DLISNGKNGQSGNEAYVTVTFKNDDGKFPDELEVVRRLKVTDDGKYSYYYLNGQRVRLSE 121 Query: 112 VVDELNKH 119 + D L Sbjct: 122 IHDFLAAA 129 >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 = 32.9 bits (75), Expect = 0.16 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%) Query: 288 STGEQKVVL-VGIFLA-HARLISNTTGFAP-ILLLDEISAHLDEDKRNALFRIVTDIGSQ 344 S GE+ + L V +F A + AP ++LLDE A +D++ R LF ++ + Sbjct: 1249 SGGERALALYVPLFAAASSHYTQEAYPHAPRLILLDEAFAGVDDNARAHLFGLLRALDLD 1308 Query: 345 IFMT 348 MT Sbjct: 1309 FVMT 1312 >gnl|CDD|179632 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional. Length = 248 Score = 31.8 bits (73), Expect = 0.27 Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 27/87 (31%) Query: 288 STGE-QKVVLVGIFL-------AHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVT 339 S GE Q+V L + L +L LLLDE LD ++ AL R+++ Sbjct: 128 SGGEWQRVRLAAVVLQVWPDINPAGQL----------LLLDEPMNSLDVAQQAALDRLLS 177 Query: 340 DIGSQ---IFMTGTDKSVFDSLNETAK 363 ++ Q + M+ D LN T + Sbjct: 178 ELCQQGIAVVMSSHD------LNHTLR 198 Score = 28.0 bits (63), Expect = 3.8 Identities = 11/24 (45%), Positives = 15/24 (62%) Query: 32 FVGDNGVGKTNILEAISFLSPGRG 55 VG NG GK+ +L ++ L PG G Sbjct: 27 LVGPNGAGKSTLLARMAGLLPGSG 50 >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 = 32.0 bits (73), Expect = 0.28 Identities = 17/43 (39%), Positives = 28/43 (65%), Gaps = 1/43 (2%) Query: 6 KIKFLNISEFRNYA-SLRLVFDAQHTIFVGDNGVGKTNILEAI 47 ++K L ++ F+++A + FD T VG NG GK+NI++AI Sbjct: 1 RLKKLELAGFKSFADPTTINFDKGITGIVGPNGCGKSNIVDAI 43 >gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein YbbL; Provisional. Length = 225 Score = 31.6 bits (72), Expect = 0.33 Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 4/36 (11%) Query: 306 LISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341 LI N +LLLDEI++ LDE + V +I Sbjct: 148 LIRNLQFMPKVLLLDEITSALDESNK----HNVNEI 179 >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 = 31.6 bits (71), Expect = 0.36 Identities = 12/24 (50%), Positives = 16/24 (66%) Query: 30 TIFVGDNGVGKTNILEAISFLSPG 53 TI VG NG GKT I+E + ++ G Sbjct: 31 TILVGPNGAGKTTIIECLKYICTG 54 >gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD. Length = 529 Score = 31.1 bits (71), Expect = 0.44 Identities = 11/25 (44%), Positives = 16/25 (64%) Query: 314 APILLLDEISAHLDEDKRNALFRIV 338 AP+LLLDE +AHLD + + + Sbjct: 477 APLLLLDEPTAHLDAETEALVTEAL 501 >gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Length = 529 Score = 30.8 bits (70), Expect = 0.53 Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 5/37 (13%) Query: 301 LAHAR-LISNTTGFAPILLLDEISAHLDEDKRNALFR 336 LA AR L+++ APILLLDE + HLD + L Sbjct: 479 LALARALLAD----APILLLDEPTEHLDAGTESELLE 511 >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 = 29.6 bits (66), Expect = 1.4 Identities = 29/101 (28%), Positives = 38/101 (37%), Gaps = 5/101 (4%) Query: 252 FDGRKMDSMSRRTLIGPHRSDLIVD--YCDKAITIAHGSTGEQKVVLVGIFLAHARLISN 309 F GR DS L+V Y A S GE + + + LA A L+S Sbjct: 916 FHGRYADSHVNAR--KYQGLALLVADAYTGSVRPSATLSGGETFLASLSLALALADLLST 973 Query: 310 TTGFA-PILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTG 349 + G L +DE LDED + I+ I M G Sbjct: 974 SGGTVLDSLFIDEGFGSLDEDSLDRAIGILDAIREGSKMIG 1014 Score = 28.0 bits (62), Expect = 4.2 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 13/85 (15%) Query: 25 FDAQHTIFV--GDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGM 82 F A IF+ G G GKT +L+AI++ G+ R S + Sbjct: 22 FTALGPIFLICGKTGAGKTTLLDAITYALYGK-LPRRSEVIRSLNS-------LYAAPSE 73 Query: 83 EGLADISIKLET---RDDRSVRCLQ 104 A++ L T R R++RC + Sbjct: 74 AAFAELEFSLGTKIYRVHRTLRCTR 98 >gnl|CDD|184128 PRK13541, PRK13541, cytochrome c biogenesis protein CcmA; Provisional. Length = 195 Score = 29.1 bits (65), Expect = 1.8 Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 9/51 (17%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338 S+G QK+V A ARLI+ + + LLDE+ +L ++ R+ L ++ Sbjct: 125 SSGMQKIV------AIARLIA---CQSDLWLLDEVETNLSKENRDLLNNLI 166 >gnl|CDD|151518 pfam11073, NSs, Rift valley fever virus non structural protein (NSs) like. This family contains several Phlebovirus non structural proteins which act as a major determinant of virulence by antagonising interferon beta gene expression. Length = 238 Score = 29.2 bits (66), Expect = 2.0 Identities = 30/142 (21%), Positives = 47/142 (33%), Gaps = 34/142 (23%) Query: 155 HRRRMIDFERLMRGRNRLLTEGYFDSSW---CSSIEAQMAELGVKINIARVEMINALSSL 211 R + DF + G F + W CSS+ + I LS Sbjct: 48 SRPTLSDF----------YSVGEFPARWGPGCSSVTKPSTKF-------FDGTIEDLSRF 90 Query: 212 IMEYVQKENFPHIKLSL---TGFLDGKF-DQSFCALKEEYAKKLFDGRKMDSMSRRTLIG 267 +E + P+IK +L G+ +F + S + Y K D ++ +G Sbjct: 91 DIESFLRSCLPNIKKALSWPLGYPSLEFFELSNI---DSY--LFLWETKCDFATQILRMG 145 Query: 268 PHRSDLIVDYCDKAITIAHGST 289 S L D +I AH Sbjct: 146 LQGSGL-----DDSIVEAHKKI 162 >gnl|CDD|182605 PRK10636, PRK10636, putative ABC transporter ATP-binding protein; Provisional. Length = 638 Score = 28.6 bits (64), Expect = 3.0 Identities = 12/19 (63%), Positives = 14/19 (73%) Query: 316 ILLLDEISAHLDEDKRNAL 334 +LLLDE + HLD D R AL Sbjct: 451 LLLLDEPTNHLDLDMRQAL 469 >gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA. Length = 731 Score = 28.1 bits (63), Expect = 3.4 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 31 IFVGDNGVGKTNILE 45 + VG+ GVGKT I E Sbjct: 207 LLVGEPGVGKTAIAE 221 >gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed. Length = 486 Score = 28.1 bits (63), Expect = 3.5 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 21/71 (29%) Query: 73 FSTFARVE-GMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDR 131 F F RVE G+EGL IS + + R +++ + V++V DE+ V +D Sbjct: 307 FGAFVRVEEGIEGLVHIS-------ELAERHVEVPEQVVQVGDEV--------FVKVID- 350 Query: 132 IFSGLSMERRR 142 + +ERRR Sbjct: 351 ----IDLERRR 357 >gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This model describes the photoreceptor protein (rim protein) in eukaryotes. It is the member of ABC transporter superfamily. Rim protein is a membrane glycoprotein which is localized in the photoreceptor outer segment discs. Mutation/s in its genetic loci is implicated in the recessive Stargardt's disease. Length = 2272 Score = 28.1 bits (62), Expect = 3.8 Identities = 12/28 (42%), Positives = 17/28 (60%) Query: 25 FDAQHTIFVGDNGVGKTNILEAISFLSP 52 ++ Q T F+G NG GKT L ++ L P Sbjct: 954 YENQITAFLGHNGAGKTTTLSILTGLLP 981 >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 = 3.9 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 4/49 (8%) Query: 300 FLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348 FL A PI++L++I DED I +IG Q+ MT Sbjct: 59 FLVVA----EAQNIEPIIVLNKIDLLDDEDMEKEQLDIYRNIGYQVLMT 103 >gnl|CDD|179591 PRK03545, PRK03545, putative arabinose transporter; Provisional. Length = 390 Score = 27.9 bits (63), Expect = 4.6 Identities = 12/29 (41%), Positives = 16/29 (55%) Query: 299 IFLAHARLISNTTGFAPILLLDEISAHLD 327 + LA A I NTT F P+ LL +I+ Sbjct: 12 VTLALAAFIFNTTEFVPVGLLSDIAQSFH 40 >gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking. Length = 164 Score = 27.9 bits (63), Expect = 5.0 Identities = 8/15 (53%), Positives = 13/15 (86%) Query: 31 IFVGDNGVGKTNILE 45 I +GD+GVGK+++L Sbjct: 4 ILIGDSGVGKSSLLS 18 >gnl|CDD|162147 TIGR00990, 3a0801s09, mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70). Length = 615 Score = 27.6 bits (61), Expect = 5.1 Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 2/33 (6%) Query: 221 FPHIKLSLTGFLDGKFDQSFCALKEEYAKKLFD 253 F HI+L +T + +G S + KK F Sbjct: 434 FSHIQLGVTQYKEGSIASSMATFRR--CKKNFP 464 >gnl|CDD|150993 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export. Length = 386 Score = 27.6 bits (62), Expect = 5.2 Identities = 9/23 (39%), Positives = 12/23 (52%) Query: 25 FDAQHTIFVGDNGVGKTNILEAI 47 + QH + VG G GKT L + Sbjct: 13 SETQHILIVGTTGTGKTQALREL 35 >gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed. Length = 298 Score = 27.5 bits (62), Expect = 5.7 Identities = 11/39 (28%), Positives = 20/39 (51%) Query: 9 FLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAI 47 L+ E L+ + + T+ G +GVGK+ +L A+ Sbjct: 146 ELSAKEGEGLDELKPLLAGKVTVLAGQSGVGKSTLLNAL 184 >gnl|CDD|149065 pfam07793, DUF1631, Protein of unknown function (DUF1631). The members of this family are sequences derived from a group of hypothetical proteins expressed by certain bacterial species. The region concerned is approximately 440 amino acid residues in length. Length = 729 Score = 27.6 bits (62), Expect = 5.8 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 26/95 (27%) Query: 85 LADISIKLETRDDRSVRCL--QINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSMERRR 142 +A+ I DD L +I ++V R+++E + +F+ L E + Sbjct: 407 IAEAGIGWGGDDDGLRDSLYAKIEEIVQRILNEFDDDP----------SLFAELLEEFQA 456 Query: 143 FLDRMVFAIDPRHR-----RRMIDFERLMRGRNRL 172 FL++ R R +R + E GR RL Sbjct: 457 FLEQE------RRRSELVEQRTREAE---EGRARL 482 >gnl|CDD|180838 PRK07102, PRK07102, short chain dehydrogenase; Provisional. Length = 243 Score = 27.6 bits (62), Expect = 6.3 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 2/51 (3%) Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNAL 334 IA G+ G+Q A A T PI LL ++ + + Sbjct: 82 IAVGTLGDQAACEAD--PALALREFRTNFEGPIALLTLLANRFEARGSGTI 130 >gnl|CDD|178142 PLN02527, PLN02527, aspartate carbamoyltransferase. Length = 306 Score = 27.4 bits (61), Expect = 6.5 Identities = 11/22 (50%), Positives = 14/22 (63%) Query: 315 PILLLDEISAHLDEDKRNALFR 336 P+ LDEI+ +D D R A FR Sbjct: 265 PLPRLDEITTDVDSDPRAAYFR 286 >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 = 27.5 bits (62), Expect = 6.6 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 34 GDNGVGKTNILEAISFLSPGRG 55 G NGVGKT +L+ + L P + Sbjct: 33 GRNGVGKTTLLKTLMGLLPVKS 54 >gnl|CDD|183835 PRK12999, PRK12999, pyruvate carboxylase; Reviewed. Length = 1146 Score = 27.4 bits (62), Expect = 7.1 Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 6/37 (16%) Query: 57 RRASYADVTRIGSPSFFSTFARVEGMEGLADISIKLE 93 R Y DV+ + +P+FF G+ +I +++E Sbjct: 990 HREEYGDVSVLPTPTFF------YGLRPGEEIEVEIE 1020 >gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional. Length = 590 Score = 27.1 bits (61), Expect = 7.3 Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 5/42 (11%) Query: 314 APILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVF 355 A + LLDE SAHLD ++R A+ + + + + + Sbjct: 472 ADLYLLDEPSAHLDVEQRLAVAKAI-----RRIAEEREATAL 508 >gnl|CDD|183531 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed. Length = 426 Score = 27.2 bits (61), Expect = 7.4 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 13/81 (16%) Query: 16 RNYASLRLVFDAQHT-IFVGDNGVGKTNIL---EAISF---LSPGRGFRRASYADVTRIG 68 NY +L F + T + GD +G ++L A + L G+ + +Y VT Sbjct: 336 TNYGAL---FLGERTNVAYGDKVIGTNHVLPTSGAARYTGGLWVGKFLKTVTYQRVTDEA 392 Query: 69 SPSF---FSTFARVEGMEGLA 86 S S R+EG EG A Sbjct: 393 SAEIGEYCSRLCRLEGFEGHA 413 >gnl|CDD|178337 PLN02736, PLN02736, long-chain acyl-CoA synthetase. Length = 651 Score = 27.0 bits (60), Expect = 7.8 Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 14/68 (20%) Query: 247 YAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARL 306 Y+K L GR S + P D+ I G+TG K G+ L H L Sbjct: 201 YSKLLAQGR----SSPQPFRPPKPEDV------ATICYTSGTTGTPK----GVVLTHGNL 246 Query: 307 ISNTTGFA 314 I+N G + Sbjct: 247 IANVAGSS 254 >gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional. Length = 216 Score = 27.2 bits (60), Expect = 7.9 Identities = 9/14 (64%), Positives = 13/14 (92%) Query: 31 IFVGDNGVGKTNIL 44 + +GD+GVGK+NIL Sbjct: 16 VLIGDSGVGKSNIL 29 >gnl|CDD|131499 TIGR02446, FadI, fatty oxidation complex, beta subunit FadI. This subunit of the FadJI complex has acetyl-CoA C-acyltransferase (EC 2.3.1.16) activity, and is also known as beta-ketothiolase and fatty oxidation complex, beta subunit, and YfcY. This protein is almost always located adjacent to FadJ (TIGR02440). The FadJI complex is needed for anaerobic beta-oxidation of short-chain fatty acids in E. coli. Length = 430 Score = 26.9 bits (59), Expect = 8.6 Identities = 13/42 (30%), Positives = 17/42 (40%) Query: 13 SEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGR 54 S YA LR FD +H N T+ A+ + GR Sbjct: 242 STLAGYAKLRPAFDRKHGSVTAANSTPLTDGAAAVILMREGR 283 >gnl|CDD|184587 PRK14241, PRK14241, phosphate transporter ATP-binding protein; Provisional. Length = 258 Score = 27.0 bits (60), Expect = 8.6 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 11/51 (21%) Query: 1 MTNRIKIKFLNISEFRNYASLRLVFDAQHTI-------FVGDNGVGKTNIL 44 M RI +K LNI Y S V D I F+G +G GK+ +L Sbjct: 1 MAKRIDVKDLNIY----YGSFHAVEDVNLNIEPRSVTAFIGPSGCGKSTVL 47 >gnl|CDD|162277 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor regulator (CFTR). The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se. Length = 1490 Score = 26.8 bits (59), Expect = 8.6 Identities = 12/14 (85%), Positives = 12/14 (85%) Query: 314 APILLLDEISAHLD 327 A ILLLDE SAHLD Sbjct: 1372 AKILLLDEPSAHLD 1385 >gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional. Length = 718 Score = 26.7 bits (59), Expect = 8.9 Identities = 13/19 (68%), Positives = 13/19 (68%) Query: 316 ILLLDEISAHLDEDKRNAL 334 ILLLDE S HLD D AL Sbjct: 648 ILLLDEPSNHLDLDAVEAL 666 >gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit; Provisional. Length = 232 Score = 26.9 bits (60), Expect = 9.5 Identities = 11/27 (40%), Positives = 16/27 (59%) Query: 315 PILLLDEISAHLDEDKRNALFRIVTDI 341 PILLLDE + LD R + +V+ + Sbjct: 149 PILLLDEPFSALDPALRQEMLTLVSQV 175 >gnl|CDD|163455 TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL subfamily. Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains. Length = 634 Score = 26.9 bits (60), Expect = 9.5 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 29 HTIFVGDNGVGKTNILEAISF 49 HT+ +G GVGKT + E + Sbjct: 178 HTLVLGTTGVGKTRLAELLIT 198 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 0.326 0.139 0.402 Gapped Lambda K H 0.267 0.0746 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 6,245,335 Number of extensions: 421075 Number of successful extensions: 1383 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1369 Number of HSP's successfully gapped: 75 Length of query: 375 Length of database: 5,994,473 Length adjustment: 95 Effective length of query: 280 Effective length of database: 3,941,713 Effective search space: 1103679640 Effective search space used: 1103679640 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: 58 (26.1 bits)