RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780229|ref|YP_003064642.1| hypothetical protein CLIBASIA_00570 [Candidatus Liberibacter asiaticus str. psy62] (1775 letters) >gnl|CDD|161845 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. Length = 637 Score = 66.4 bits (162), Expect = 6e-11 Identities = 65/297 (21%), Positives = 116/297 (39%), Gaps = 69/297 (23%) Query: 1358 KDVKFDLVIMDESSQIKPEDALGVIARGKQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVA 1417 K +FD+ ++DE+SQ L + + +++++ GD KQLPPT HD ++ Sbjct: 358 KGWEFDVAVIDEASQAMEPSCLIPLLKARKLILAGDHKQLPPT-ILSHDAEE-------- 408 Query: 1418 AVSQTESILDALLPLFSMRR--LQWHYRSLNENLIACSNYYFYDNSLIVFPS-------- 1467 ++ + L+ + R L YR +N+ ++ + FY+ L S Sbjct: 409 ---LELTLFERLIKEYPERSRTLNVQYR-MNQKIMEFPSREFYNGKLTAHESVANILLRD 464 Query: 1468 -----------------PYTSVDRYGVGFTHVKNGVVVDQGNPEEARVIALAVKDHALRY 1510 P +D G +K + NP EA +++ ++ ++ Sbjct: 465 LPKVEATDSEDDLETEIPLLFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQA-LVKM 523 Query: 1511 --PEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDE 1568 P +GVI Q DL+ + + ++E + +++ QG E Sbjct: 524 GVPANDIGVITPYDAQVDLLRQLLEH---RHIDIE--------------VSSVDGFQGRE 566 Query: 1569 RDRIFISFTYGPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDV 1625 ++ I ISF R G + RRLNV TR+RR++ V R L Sbjct: 567 KEVIIISFVRS---------NRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSN 614 Score = 60.6 bits (147), Expect = 4e-09 Identities = 67/296 (22%), Positives = 119/296 (40%), Gaps = 43/296 (14%) Query: 316 IEESKSHWAVRRYGVLGLLNFSKMLMYLDLDHLRWPEGEDNIL-NHDIIQRLFIAQSCDH 374 +EES W+++R + N D+ R E + NH + + + Sbjct: 92 LEESVPQWSLKRVRIDLYAN--------DVTFKRMKEALRALTENHSRLLEFILGREAPS 143 Query: 375 DKDNASSNQNIEYKIDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNL-IIEGPPGTGKS 433 Q + ++E SQ AV ++ K+L +I GPPGTGK+ Sbjct: 144 KASEIHDFQFFDPNLNE----------------SQKEAVSFALSSKDLFLIHGPPGTGKT 187 Query: 434 QTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLEL-HSHKVHKRAILDD 492 +T+ +I + G ++L A A++ + RL A + + L H ++ K Sbjct: 188 RTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERL--ALCDQKIVRLGHPARLLKSNKQHS 245 Query: 493 LRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTELSIHQILMGAAR-- 550 L I+N + +I +I +EL + N+ + Q + LS +IL A + Sbjct: 246 LDYLIENHPKYQIVADIREKI---DELIEERNKKLKPSPQKRRG--LSDIKILRKALKKR 300 Query: 551 -YRHNLPLDPVQLHVEGLSGENADRLLRS------RLEDQIKAFKDVIVEFHKQAG 599 R L + + ++ DRLL+ R+E++I A DV+ + AG Sbjct: 301 EARGIESLKIASMAEWIETNKSIDRLLKLLPEIEERIENEILAESDVVQSTNSSAG 356 >gnl|CDD|162366 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. Length = 720 Score = 39.8 bits (93), Expect = 0.006 Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 2/51 (3%) Query: 406 DSSQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIA-AAMLHG-KKILFCA 454 Q A+ I K +I+ G PGTGK+ II A L G + A Sbjct: 325 SEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAA 375 Score = 30.9 bits (70), Expect = 3.0 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 4/53 (7%) Query: 1350 SVANYLEPKDVKFDLVIMDESSQIKPEDA---LGVIARGKQIVVVGDPKQLPP 1399 N+LE + DL+I+DESS + A L + ++++VGD QLP Sbjct: 406 FRHNHLEDP-IDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPS 457 >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 = 37.0 bits (85), Expect = 0.042 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 25/166 (15%) Query: 419 GKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLE 478 G+ ++I GPPG+GK+ + G +++ + EV+ L G+ Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKK--- 58 Query: 479 LHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTE 538 L + +D EIT + + + E ++ + Sbjct: 59 ---ASGSGELRLRLALALARKLKPDVLI--LD-EITSLLDAEQEALLLLLEELRLLLLLK 112 Query: 539 LSIHQILMGAARYRHNLPLDPVQLHVEGLSGENADRLLRSRLEDQI 584 + ++ +L LLR R + +I Sbjct: 113 SEKNLTVILTTNDEKDL----------------GPALLRRRFDRRI 142 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 36.6 bits (85), Expect = 0.065 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 16/62 (25%) Query: 421 NLIIEGPPGTGKSQTITNIIA----------AAMLHGKKILFCAQKMAAIEVVRHRLEKA 470 +LI+ GPPG GK+ T+ IIA A+L G K L A ++ + RLE+ Sbjct: 54 SLILYGPPGVGKT-TLARIIANHTRAHFSSLNAVLAGVKDL-----RAEVDRAKERLERH 107 Query: 471 GL 472 G Sbjct: 108 GK 109 >gnl|CDD|184869 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional. Length = 659 Score = 34.8 bits (80), Expect = 0.22 Identities = 47/199 (23%), Positives = 90/199 (45%), Gaps = 33/199 (16%) Query: 979 FKRIQKLHCDELSKKITKVFGRIQELEQFLPKQKELQN-RSALFVGEGNVFDSLIQ-RLS 1036 ++ + ELS+ TK RI+ELE+++ + L+N R ++F +D+++ L+ Sbjct: 251 SSKVSSMLNSELSRVTTK---RIKELEEYVLRDLLLENYRDSVF------WDTVVSCYLN 301 Query: 1037 HN----FDPWQNWFKEDEI-----LLQEAQEFSAKLHKIREKNIVLAEESLIKKFFGEEI 1087 + FD + ++F + EI L+ E +L K +V+ E L K EEI Sbjct: 302 FDFTKYFDKYGHYFDKKEIEDVKMLINGLPESLGELKTYCLKYLVM--EYLFNKLDEEEI 359 Query: 1088 KLSVFDSNTKESNKSLAVINSTLEFAH-SIRERVLFDELIQGINHIDDHTIYNSFIKDLK 1146 K + N + +E+A + L DE + + +I F+K+LK Sbjct: 360 K--------EIKNHFKKKPENFMEWAEKNYLNASLLDEFRKKVKNITKSP--EEFVKELK 409 Query: 1147 NLRMIWQQQVKTQEDFIED 1165 + M+ ++++ I+D Sbjct: 410 DKAMVSDEELEKYRKEIKD 428 >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed. Length = 2890 Score = 33.4 bits (76), Expect = 0.50 Identities = 22/102 (21%), Positives = 48/102 (47%), Gaps = 15/102 (14%) Query: 1060 SAKLHKIREKNIVLAE---ESLIKKFFGEEI---KLSVFDSNTKESNKSLAVINSTLEFA 1113 S K+ +++E ++ E + L+ + E + K + D T+ L I+ Sbjct: 273 SRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHD----- 327 Query: 1114 HSIRERVLFDELIQGINHIDDHTIYNSFIKDLKNLRMIWQQQ 1155 ++E V+ ++L G D +I +SF D ++L+++ Q + Sbjct: 328 LGVQEFVIINDLALGH----DASIIHSFSADSESLKLLKQTE 365 >gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional. Length = 319 Score = 33.2 bits (76), Expect = 0.62 Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 20/85 (23%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMA----------AIEVVRHRL 467 N NLI+ GPPGTGK+ T+I+A A ++L K A I+VVR+++ Sbjct: 33 NMPNLILSGPPGTGKT---TSILALA----HELLGPNYKEAVLELNASDDRGIDVVRNKI 85 Query: 468 EKAGLGEFCLELHSHKVHKRAILDD 492 + + L HK+ ILD+ Sbjct: 86 KMFAQKKVTLPPGRHKI---VILDE 107 >gnl|CDD|148013 pfam06152, Phage_min_cap2, Phage minor capsid protein 2. Family of related phage minor capsid proteins. Length = 361 Score = 32.0 bits (73), Expect = 1.3 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 2/73 (2%) Query: 140 IREIEKKIEISLQKLTSIIQNYGYADIEDLERAIKE--NKPLKPPHFQNNLSDNQIQTAY 197 I+ I K ++ + +T +I+N G I+D+++ + E NK L N + Sbjct: 65 IKLIAKYTGVAEEAITRVIKNAGLKIIKDIDKQLSEALNKGLGADPESNFQTIVDKVLNA 124 Query: 198 FQDKLESILRLIN 210 +Q + S L L+N Sbjct: 125 YQRQAWSDLNLVN 137 >gnl|CDD|163008 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer. Length = 744 Score = 31.7 bits (72), Expect = 1.5 Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 4/41 (9%) Query: 1363 DLVIMDESSQIKPEDALGVIA----RGKQIVVVGDPKQLPP 1399 D++++DE+ + V+ G ++V+VGDP+QL P Sbjct: 441 DVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQP 481 >gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated. Length = 269 Score = 31.8 bits (72), Expect = 1.6 Identities = 15/35 (42%), Positives = 21/35 (60%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452 G NL++ GPPG GKS I A + +G ++LF Sbjct: 105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLF 139 >gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional. Length = 254 Score = 31.8 bits (72), Expect = 1.7 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%) Query: 406 DSSQHSAVIDVINGK-NLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452 D+ H +D + GK N++ GPPGTGK+ + A G ++LF Sbjct: 84 DTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLF 131 >gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed. Length = 413 Score = 31.6 bits (73), Expect = 1.9 Identities = 13/24 (54%), Positives = 18/24 (75%), Gaps = 1/24 (4%) Query: 421 NLIIEGPPGTGKSQTITNIIAAAM 444 ++I+ GPPGTGK+ T+ IIA A Sbjct: 38 SMILWGPPGTGKT-TLARIIAGAT 60 >gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. Length = 395 Score = 31.5 bits (72), Expect = 2.0 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 9/55 (16%) Query: 417 INGKNLIIEGPPGTGKSQTITNIIAAAMLH--GKKILFCAQKMAAIEVVRHRLEK 469 I G+ ++I GPPGTGK+ +A A+ G+ FC ++ EV ++K Sbjct: 48 IAGRAVLIAGPPGTGKTA-----LAIAISKELGEDTPFCP--ISGSEVYSLEMKK 95 >gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. Length = 850 Score = 31.3 bits (71), Expect = 2.1 Identities = 53/246 (21%), Positives = 86/246 (34%), Gaps = 46/246 (18%) Query: 977 QLFKRIQKLHCDELSKKI----TKVFGRIQELEQFLPKQKELQNRSALFVGEGNVFDSLI 1032 QL KRIQ+L E+ +K+ TK + + K LQ S L D L Sbjct: 483 QLLKRIQQLEKQEILEKLFDFETKDILKDLQAIL-DKLNKLLQIFSELSH---KTVDQLR 538 Query: 1033 ---QRLSHNFDPWQNWFKEDEILLQEAQEFSAKLHKIREKNIVLAEESLIKKFFGEEIKL 1089 L +F + KE + K + L K+ Sbjct: 539 KFDLALKDDFKNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLL------ 592 Query: 1090 SVFDSNTKESNKSLAVINSTLEFAHSIRERVLFDELIQGINHIDDH--TIYNSFIKDLKN 1147 KSL ++TL+F+HS F+ Q + D H TI + + +N Sbjct: 593 --------PKFKSLIFTSATLKFSHS------FESFPQLLGLTDVHFNTIEPTPLNYAEN 638 Query: 1148 LRMIWQQQVKTQEDFIEDTQLDMAQWAARCNDELVKLISRNSEAIKKPRWLNGWVN--LM 1205 Q+V D + ++A ++++ AI P+ L + + ++ Sbjct: 639 ------QRVLIPTDAPAIQNKSLEEYAQEIASYIIEI-----TAITSPKILVLFTSYEML 687 Query: 1206 HMVQDM 1211 HMV DM Sbjct: 688 HMVYDM 693 >gnl|CDD|180288 PRK05850, PRK05850, acyl-CoA synthetase; Validated. Length = 578 Score = 31.5 bits (72), Expect = 2.3 Identities = 34/112 (30%), Positives = 47/112 (41%), Gaps = 29/112 (25%) Query: 1463 IVFPSPYTSVD---RYG-VGFTH---------VKNGVVVDQGN--PE--EA--------R 1497 +V PSP T R G +GF +K+ ++VD N P+ EA R Sbjct: 426 LVDPSPGTPEGPWLRTGDLGFISEGELFIVGRIKDLLIVDGRNHYPDDIEATIQEITGGR 485 Query: 1498 VIALAVKDHALRYPEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKL 1549 V A++V D E L I K+ D E +++L EV AISK Sbjct: 486 VAAISVPDDG----TEKLVAIIELKKRGDSDEEAMDRLRTVKREVTSAISKS 533 >gnl|CDD|128765 smart00489, DEXDc3, DEAD-like helicases superfamily. Length = 289 Score = 31.2 bits (71), Expect = 2.4 Identities = 25/119 (21%), Positives = 45/119 (37%), Gaps = 31/119 (26%) Query: 418 NGKNLIIEGPPGTGKSQT-ITNIIAAAMLHGKKILFCAQKMAAIEVVR--HRLEKAGLGE 474 GK I+E P GTGK+ + + + ++I QK+ I + R +EK Sbjct: 26 RGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI----QKIKLIYLSRTVSEIEKR---- 77 Query: 475 FCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQI 533 L++LRK + E D E + +L +L + ++ + Sbjct: 78 ---------------LEELRKLMQKV-----EYESDEESEKQAQLLHELGREKPKVLGL 116 >gnl|CDD|128764 smart00488, DEXDc2, DEAD-like helicases superfamily. Length = 289 Score = 31.2 bits (71), Expect = 2.4 Identities = 25/119 (21%), Positives = 45/119 (37%), Gaps = 31/119 (26%) Query: 418 NGKNLIIEGPPGTGKSQT-ITNIIAAAMLHGKKILFCAQKMAAIEVVR--HRLEKAGLGE 474 GK I+E P GTGK+ + + + ++I QK+ I + R +EK Sbjct: 26 RGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI----QKIKLIYLSRTVSEIEKR---- 77 Query: 475 FCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQI 533 L++LRK + E D E + +L +L + ++ + Sbjct: 78 ---------------LEELRKLMQKV-----EYESDEESEKQAQLLHELGREKPKVLGL 116 >gnl|CDD|184408 PRK13937, PRK13937, phosphoheptose isomerase; Provisional. Length = 188 Score = 31.4 bits (72), Expect = 2.4 Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 8/42 (19%) Query: 439 IIAAAMLHGKKILFC--------AQKMAAIEVVRHRLEKAGL 472 + A+ +G KIL C AQ +AA V R + E+ L Sbjct: 30 ALIEALANGGKILLCGNGGSAADAQHIAAELVGRFKKERPAL 71 >gnl|CDD|162365 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. Length = 586 Score = 30.9 bits (70), Expect = 3.1 Identities = 12/34 (35%), Positives = 18/34 (52%) Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAA 442 Q AV + +I G PGTGK+ T+ ++ A Sbjct: 150 QKVAVALALKSNFSLITGGPGTGKTTTVARLLLA 183 >gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed. Length = 279 Score = 30.9 bits (70), Expect = 3.4 Identities = 14/32 (43%), Positives = 17/32 (53%) Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 + G G GKS T+ NI AA GKK+L Sbjct: 2 RKFCFYGKGGIGKSTTVCNIAAALAESGKKVL 33 >gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein; Provisional. Length = 235 Score = 30.8 bits (70), Expect = 3.7 Identities = 21/105 (20%), Positives = 38/105 (36%), Gaps = 22/105 (20%) Query: 1135 HTIYNSFIKDLKNLRMIWQQQVKTQEDFIEDTQLDMAQWAARCNDELVKLISRNSEAIKK 1194 H Y D ++ + W LD+ ++ +K +S + Sbjct: 30 HATYRHHKPDFQHDNVQWHA-------------LDV------TDEAEIKQLSEQFTQLD- 69 Query: 1195 PRWLNGWVNLMHMVQDMQDKGLKEIQAAIFNNSLDVKYLESSLLA 1239 WL V ++H +K L+ + A F ++ + L S LLA Sbjct: 70 --WLINCVGMLHTQDKGPEKSLQALDADFFLQNITLNTLPSLLLA 112 >gnl|CDD|153048 pfam12614, RRF_GI, Ribosome recycling factor. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression. Length = 128 Score = 30.4 bits (69), Expect = 3.9 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%) Query: 1725 DRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELRELISQKSSST 1773 D+L+ E E + IR+I + + +EP+ +L LI Q + T Sbjct: 58 DQLKTEEYEEFRYLIRKIEAA--LLLHSDKLEPLEDKLIRLIPQNPNIT 104 >gnl|CDD|161955 TIGR00608, radc, DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 218 Score = 30.5 bits (69), Expect = 4.2 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 15/69 (21%) Query: 627 SSLENWQSALIKWQKD--HE-------VFLNRYGVQNQRQRLLYWQGQLLAAVDQVPSLP 677 + + ++A D HE +FL+R + RL+ + + V+ VP P Sbjct: 95 PVIRSPEAAAEFLHTDLAHETREHFMVLFLDR------KNRLIAKEVVFIGTVNHVPVHP 148 Query: 678 RVICFKAFK 686 R I +A K Sbjct: 149 REIFKEALK 157 >gnl|CDD|162286 TIGR01287, nifH, nitrogenase iron protein. This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase. Length = 275 Score = 30.4 bits (69), Expect = 4.3 Identities = 14/32 (43%), Positives = 18/32 (56%) Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 + + I G G GKS T NI AA GKK++ Sbjct: 1 RQIAIYGKGGIGKSTTTQNIAAALAEMGKKVM 32 >gnl|CDD|183073 PRK11281, PRK11281, hypothetical protein; Provisional. Length = 1113 Score = 30.3 bits (69), Expect = 4.4 Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 12/50 (24%) Query: 15 DMRRKLLDCSVQ-NKLL--------NFRMDQQSVLRIFNTSPNQLYQQIF 55 D RR+LLD Q NK L N +++QQ +L + ++ + L QQIF Sbjct: 410 DERRELLD---QLNKQLNNQLNLAINLQLNQQQLLSVSDSLQSTLTQQIF 456 >gnl|CDD|178717 PLN03173, PLN03173, chalcone synthase; Provisional. Length = 391 Score = 30.4 bits (68), Expect = 4.5 Identities = 13/36 (36%), Positives = 20/36 (55%) Query: 1234 ESSLLAAIYHQLSQEILTEKPHLMHYSAVQFTAKQE 1269 E S++ Y L++EIL E P + Y A A+Q+ Sbjct: 61 EKSMIKKRYMHLTEEILKENPSVCEYMAPSLDARQD 96 >gnl|CDD|182067 PRK09767, PRK09767, hypothetical protein; Provisional. Length = 117 Score = 30.4 bits (68), Expect = 4.6 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%) Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIREL 1762 +E DG ++ A + R R LE GW + R W+ + N + V+E I++EL Sbjct: 59 VELDGGQHDLAVAYDTR---RTSWLESQGWTVLRFWNNEIDCNEEAVLEIILQEL 110 >gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional. Length = 880 Score = 30.0 bits (68), Expect = 5.0 Identities = 19/91 (20%), Positives = 47/91 (51%), Gaps = 17/91 (18%) Query: 107 EYDSDDEKKNYQVLQKVRDL----------IVEDIKTSNDLV-DIREIEKKI---EISLQ 152 +Y+ ++ +K + +K+++ + ++++ +L + E+EKK+ E L Sbjct: 514 KYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEEELA 573 Query: 153 KLTSIIQNYGYADIEDLERAIKENKPLKPPH 183 +L ++ G+ +E+LE +KE L+P + Sbjct: 574 ELLKELEELGFESVEELEERLKE---LEPFY 601 >gnl|CDD|185348 PRK15451, PRK15451, tRNA cmo(5)U34 methyltransferase; Provisional. Length = 247 Score = 30.0 bits (67), Expect = 5.6 Identities = 12/31 (38%), Positives = 19/31 (61%) Query: 1100 NKSLAVINSTLEFAHSIRERVLFDELIQGIN 1130 N S+ V+N TL+F + L D++ QG+N Sbjct: 125 NASMVVLNFTLQFLEPSERQALLDKIYQGLN 155 >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 = 29.9 bits (68), Expect = 5.7 Identities = 8/32 (25%), Positives = 18/32 (56%) Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 ++++I G GTGK+Q + ++ G + + Sbjct: 16 QHILIVGTTGTGKTQALRELLDQIRARGDRAI 47 >gnl|CDD|130348 TIGR01281, DPOR_bchL, light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein. The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit. Length = 268 Score = 29.8 bits (67), Expect = 5.9 Identities = 12/30 (40%), Positives = 17/30 (56%) Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 L + G G GKS T +N+ A GK++L Sbjct: 3 LAVYGKGGIGKSTTSSNLSVAFAKLGKRVL 32 >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 = 29.9 bits (67), Expect = 6.0 Identities = 24/176 (13%), Positives = 51/176 (28%), Gaps = 8/176 (4%) Query: 515 RYEELKGQLNQYAQEINQIWKNTELSIHQILMGAARYRHNLPLDPVQLHVEGLSGENADR 574 K Q Q Q++ + + L + L + V+ H + R Sbjct: 615 HALLRKLQPEQDLQDVRLHLQQCSQELALKLTALHALQLTLTQERVREHAL------SIR 668 Query: 575 LLRSRLEDQIKAFKDVIVEFHKQAGESMELMNHPWYGVHSSDIHILNYNKALSSLENWQS 634 +L L + + +Q E++ + + HI Y++ + +EN S Sbjct: 669 VLPKELLASRQLALQKMQSEKEQLTYWKEMLAQCQTLLRELETHIEEYDREFNEIENASS 728 Query: 635 ALIKWQKDHEVFLNRYGVQNQRQRLLYWQGQLLAAVDQVPSLPRVICFKAFKKLED 690 +L E LN+ + + + + +L Sbjct: 729 SLGSDLAAREDALNQ--SLKELMHQARTVLKARTEAHFNNNEEVTAALQTGAELSH 782 >gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 139 Score = 30.0 bits (68), Expect = 6.0 Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%) Query: 421 NLIIEGPPGTGKSQTITNIIAAAM 444 +++ GPPGTGKS + +AAA+ Sbjct: 1 GVLLVGPPGTGKS-ELAERLAAAL 23 >gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase domain-containing protein; Reviewed. Length = 229 Score = 29.9 bits (68), Expect = 6.8 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 11/60 (18%) Query: 386 EYKIDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNLI--IEGPPGTGKSQTITNIIAAA 443 +Y+ +EIE +H+ PL+ + A + + I I GPPG GKS T+ + A Sbjct: 6 QYRDEEIEAVHK--PLL------RRLAALQAEPQRRTIVGIAGPPGAGKS-TLAEFLEAL 56 >gnl|CDD|182715 PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional. Length = 413 Score = 29.7 bits (67), Expect = 7.0 Identities = 34/133 (25%), Positives = 54/133 (40%), Gaps = 38/133 (28%) Query: 434 QTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLELHSHKVHKRAILDDL 493 Q I NI AQ ++ +R RL GL + +++ K I+ ++ Sbjct: 80 QAIANI-------------AAQNNMTLDQMRSRLAYDGLN---YNTYRNQIRKEMIISEV 123 Query: 494 RKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEI-NQIWKNTELSIHQILMGAARYR 552 R R I +PQE+D A++I NQ +TEL++ IL+ Sbjct: 124 RNNEVRRRITILPQEVD--------------SLAKQIGNQNDASTELNLSHILI------ 163 Query: 553 HNLPLDPVQLHVE 565 LP +P Q V+ Sbjct: 164 -PLPENPTQDQVD 175 >gnl|CDD|181881 PRK09466, metL, bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional. Length = 810 Score = 29.5 bits (67), Expect = 7.1 Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 25/115 (21%) Query: 950 YRKVHQIWKDNSSLDDALINGFLMLDS-------QLFKRIQKLHCDELSKKITKVFGRIQ 1002 YR+V I + S DD L++ S QL ++ D LS Q Sbjct: 28 YRRVAGILAEYSQPDD------LVVVSAAGKTTNQLISWLKLSQTDRLSAHQV-----QQ 76 Query: 1003 ELEQFLPKQKELQNRSALFVGEGNVFDSLIQRLSHNFDPWQNWFKEDEILLQEAQ 1057 L ++ Q++L L SL+ RL + + Q A+ Sbjct: 77 TLRRY---QQDLI--EGLL--PAEQARSLLSRLISDLERLAALLDGGINDAQYAE 124 >gnl|CDD|163318 TIGR03545, TIGR03545, conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair. Length = 555 Score = 29.7 bits (67), Expect = 7.7 Identities = 23/125 (18%), Positives = 42/125 (33%), Gaps = 16/125 (12%) Query: 900 WKKLYAQLPNAYQFAVEKEKLEKRNFGNTLGEHYRGLSTDIVALKNIREWYRKVHQIWKD 959 WKK LPN K++LE + + DI +++ + ++ K+ Sbjct: 180 WKKRKKDLPNKQDLEEYKKRLE------AIKK------KDIKNPLELQKIKEEFDKLKKE 227 Query: 960 NSSLDDALINGFLMLDSQLFKRIQKLHCDELSKKITKVFGRIQELEQFLPKQKELQNRSA 1019 D I K+++ EL K R++ K +L+N + Sbjct: 228 -GKADKQKIKSAKNDLQNDKKQLKAD-LAELKKAPQNDLKRLENKYAI--KSGDLKNFAV 283 Query: 1020 LFVGE 1024 G Sbjct: 284 DLFGP 288 >gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed. Length = 337 Score = 29.6 bits (67), Expect = 7.8 Identities = 8/19 (42%), Positives = 15/19 (78%) Query: 418 NGKNLIIEGPPGTGKSQTI 436 N +L+++GPPG+GK+ + Sbjct: 35 NLPHLLVQGPPGSGKTAAV 53 >gnl|CDD|140295 PTZ00269, PTZ00269, variant surface glycoprotein; Provisional. Length = 472 Score = 29.5 bits (66), Expect = 7.9 Identities = 19/44 (43%), Positives = 27/44 (61%), Gaps = 6/44 (13%) Query: 1041 PW----QNWFKEDEILLQEAQEFSAKLHKIREKNIVLAEESLIK 1080 PW + E E+LLQ+ Q+ SAKL +I+E + + ESLIK Sbjct: 325 PWMKALEKVENEMEVLLQDKQDKSAKLERIKELSQEI--ESLIK 366 >gnl|CDD|180003 PRK05302, PRK05302, 30S ribosomal protein S7; Validated. Length = 156 Score = 29.7 bits (68), Expect = 7.9 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%) Query: 432 KSQTITNIIAAAMLHGKKILFCAQKM--AAIEVVRHRLEKAGL 472 S +T I ML GKK + A+K+ A++++ + K L Sbjct: 19 GSVLVTKFINKLMLDGKKSV--AEKIVYGALDIIEEKTGKDPL 59 >gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed. Length = 328 Score = 29.3 bits (67), Expect = 8.0 Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%) Query: 426 GPPGTGKSQTITNIIAAAM 444 GPPG GK+ T+ NIIA M Sbjct: 58 GPPGLGKT-TLANIIANEM 75 >gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated. Length = 234 Score = 29.6 bits (67), Expect = 8.3 Identities = 12/31 (38%), Positives = 17/31 (54%) Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452 ++IEG GTGKS + A+ GKK+ Sbjct: 28 ILIEGDHGTGKSVLSQQFVYGALKQGKKVYV 58 >gnl|CDD|162859 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis. Length = 633 Score = 29.3 bits (66), Expect = 8.8 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 9/83 (10%) Query: 1472 VDRYGVGFTHVKNGVVVDQGNPEEARV-------IALAVKDHALRYPEESLGVIAMN-AK 1523 V+R G+ +H V++ NPEE + L V A R PEE + +I A Sbjct: 157 VEREGLSVSHPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEIIRRRLAF 216 Query: 1524 QRDLIESTINKLCRKDSEVEKAI 1546 D E+ + + E+ I Sbjct: 217 DADP-EAFAARWAAEQEELRNRI 238 >gnl|CDD|185583 PTZ00375, PTZ00375, dihydroxyacetone kinase-like protein; Provisional. Length = 584 Score = 29.4 bits (66), Expect = 9.2 Identities = 11/46 (23%), Positives = 14/46 (30%), Gaps = 3/46 (6%) Query: 890 LSLAKNPGISWKKLYAQLPN-AYQFAVEKEKLEKRNFGNTLGEHYR 934 L P SW A+ P A Q A + + R R Sbjct: 336 LLNFHTPQSSWA--TAKGPLSALQLAKPEAEAASRKAATPTNSLLR 379 >gnl|CDD|179887 PRK04863, mukB, cell division protein MukB; Provisional. Length = 1486 Score = 29.2 bits (66), Expect = 9.4 Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 21/100 (21%) Query: 255 LEKRSSTSQPGLTQYHLRYTGEEIILNLSLKEKLQSDFGIILPAIAEGMWPEDYFLQIQK 314 L R S ++ Q + T E ++ +L +KL+ E DY ++++ Sbjct: 1065 LHARLSANRSRRNQLEKQLTFCEAEMD-NLTKKLRK---------LE----RDYH-EMRE 1109 Query: 315 IIEESKSHW-----AVRRYGVLGLLNFSKMLMYLDLDHLR 349 + +K+ W V+ GV L+ + L YL D LR Sbjct: 1110 QVVNAKAGWCAVLRLVKDNGVERRLH-RRELAYLSADELR 1148 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 0.319 0.136 0.397 Gapped Lambda K H 0.267 0.0681 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 29,648,298 Number of extensions: 2032730 Number of successful extensions: 4945 Number of sequences better than 10.0: 1 Number of HSP's gapped: 4932 Number of HSP's successfully gapped: 97 Length of query: 1775 Length of database: 5,994,473 Length adjustment: 107 Effective length of query: 1668 Effective length of database: 3,682,417 Effective search space: 6142271556 Effective search space used: 6142271556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 64 (28.5 bits)