RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780229|ref|YP_003064642.1| hypothetical protein CLIBASIA_00570 [Candidatus Liberibacter asiaticus str. psy62] (1775 letters) >gnl|CDD|31309 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]. Length = 767 Score = 123 bits (310), Expect = 3e-28 Identities = 115/585 (19%), Positives = 217/585 (37%), Gaps = 33/585 (5%) Query: 1047 KEDEILLQEAQEFSAKLHKIREKNIV--LAEESLIKKFFGEEIKLSVFDSNTKESNKSLA 1104 K L E+ +L K+ +K I L E+ ++ E + + + L+ Sbjct: 176 KIKSELAGLLIEYLKRLRKVLDKIIPPPLFEKEEVRVDIVENLLELSESILLRRELELLS 235 Query: 1105 VINSTLEFAHSIRERVLFDELIQGINHIDDHTIYNSFIKDLKNLRMIWQQQVKTQEDFIE 1164 L+ +L + + I +D K+L N + + +++ + D Sbjct: 236 KFALILKRLLESLFEILRGKDLP-IKLLDVELELVEINKELDNEQKLAVKRLLSLNDLFL 294 Query: 1165 DTQLDMAQWAARCNDELVKLISRNSEAIKKPRWLNGWVN--LMHMVQDMQDKGLKEIQAA 1222 Q R +++LI E K N + ++++ ++ +K Sbjct: 295 IHQGPFGTGKTRSVT-ILELIIELLENNKLKILPTAESNAAVDNLLRRLKRTVIKVELLR 353 Query: 1223 IFNNSLDVKYLESSLLAAIYHQLSQEILTEKPHLMHYSAVQFTAKQERFREYDKRLQFLQ 1282 I + S +K L+ L + + + + L + RE K + L+ Sbjct: 354 IGHPSRVLKKLKLDTLEELLEKH-EIPGNKIAALDKVIRELREEGERIIREIAKLRERLE 412 Query: 1283 RQRIASVIGNQKIAQGISGGLKSDYTELSLIRSELGKKNRNIPIRQLISRAKNSLLQLKP 1342 R+R+ + +GI L + + K + + L +A +L+ Sbjct: 413 RKRLDKISHLNVALRGILPALNKSEALWISLEEKQKKILKELRR--LKKKAVTKILEAAD 470 Query: 1343 CFMMSPMSVANYLEPKDVKFDLVIMDESSQIKPEDALGVIARGKQIVVVGDPKQLPPTRF 1402 + S +S+A + K +FD VI+DE+SQ AL ++R K++++VGD KQLPPT F Sbjct: 471 VVL-STLSIAGFSILKKYEFDYVIIDEASQATEPSALIALSRAKKVILVGDHKQLPPTVF 529 Query: 1403 FDHDNDQEDYDEEVAAVSQTESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYDNSL 1462 F + + +S + + L+ YR ++ ++IA S+ FY+ L Sbjct: 530 FKESSPEG--------LSASLFERLIDNGPEVVYLLRVQYR-MHPDIIAFSSKVFYNGRL 580 Query: 1463 IVFPSP--YTSVDRYGVGFTHVKNGVVVDQGNPEEARVIALAVKDHALRYPEESLGVIAM 1520 V S +T +D D EE + + + VI Sbjct: 581 EVHTSFLAFTLLDGEIPEVVISNPLEFYDTLGAEEFFESKSKLNELEAEIVK----VIVD 636 Query: 1521 NAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFTYGP 1580 + L E+ I + ++V L + ++ QG E+D I +S Sbjct: 637 ELLKDGLEENDIGVISPYRAQVSLIRRLLNEAGKGVEVGTVDGFQGREKDVIILSLVRSN 696 Query: 1581 HEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDV 1625 + G F RRLNV TR++R++ V + L+ Sbjct: 697 DDKGEIGFLG--------DPRRLNVALTRAKRKLIVVGSSSTLES 733 >gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication, recombination and repair]. Length = 1100 Score = 65.4 bits (159), Expect = 1e-10 Identities = 66/314 (21%), Positives = 112/314 (35%), Gaps = 71/314 (22%) Query: 1361 KFDLVIMDESSQIKPEDALGVIARGKQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVAAVS 1420 +FD I+DE+SQI LG ++ + V+VGD QLPP +E + S Sbjct: 796 QFDYCIIDEASQILLPLCLGPLSFSNKFVLVGDHYQLPPLVRSSEAR------QEGLSES 849 Query: 1421 QTESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYDNSLI----------------- 1463 + + + S LQ YR +N ++ SN Y N L Sbjct: 850 LFKRLSEKHPEAVSSLTLQ--YR-MNREIMRLSNKLIYGNRLKCGSKEVSRASELDRKGA 906 Query: 1464 -VFPSPYTSVDRYGVGFTHVKNGVVV-------------DQG---NPEEARVIALAVKDH 1506 +S D + V ++G N EA++I+ V+D Sbjct: 907 LSVYMDDSSSDHWLQAVLEPTRDVCFVNTDTCSTIESQGEKGGITNHGEAKLISELVEDF 966 Query: 1507 ALR-YPEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQ 1565 +G+I+ Q +LI ++ I ++ Q Sbjct: 967 VKSGVKPSDIGIISPYRAQVELIRKILSS-------------------AVLEINTVDRYQ 1007 Query: 1566 GDERDRIFISFTYGPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDV 1625 G ++D I +SF + + G + D WRRLNV TR+++++ + + L+ Sbjct: 1008 GRDKDCIIVSFVRSNKK------SKVGELLKD--WRRLNVALTRAKKKLILVGSKSTLES 1059 Query: 1626 VVDIDSKLGIRVMR 1639 L + R Sbjct: 1060 YPPFRQLLKLLENR 1073 Score = 46.1 bits (109), Expect = 9e-05 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%) Query: 409 QHSAVIDVINGKN-LIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRL 467 Q A++ + ++ +I G PGTGK+ TI+ +I + GKK+L + +A++ + +L Sbjct: 674 QRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALGKKVLLTSYTHSAVDNILIKL 733 Query: 468 EKAGLGEFCLELHSHKVHK 486 + G+ L K+H Sbjct: 734 KGFGIYILRLG-SEEKIHP 751 >gnl|CDD|37014 KOG1803, KOG1803, KOG1803, DNA helicase [Replication, recombination and repair]. Length = 649 Score = 60.8 bits (147), Expect = 4e-09 Identities = 41/132 (31%), Positives = 67/132 (50%), Gaps = 4/132 (3%) Query: 393 EDIHQRCPLIDDSDSSQHSAVIDVINGKNL-IIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 +I + + +SSQ +AV IN K+L II GPPGTGK++T+ II+ + K++L Sbjct: 174 IEIKKITFFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKKRVL 233 Query: 452 FCAQKMAAIEVVRHRLEKAGLGEFCLELHSHKVHKRAI--LDDLRKRIDN-RNIKTVPQE 508 CA A++ + RL L + + + A LD L DN +N K + ++ Sbjct: 234 VCAPSNVAVDNIVERLTHLKLNLVRVGHPARLLESVADHSLDLLSNTKDNSQNAKDISKD 293 Query: 509 IDVEITRYEELK 520 ID+ + + K Sbjct: 294 IDILFQKNTKTK 305 Score = 60.0 bits (145), Expect = 6e-09 Identities = 81/339 (23%), Positives = 127/339 (37%), Gaps = 81/339 (23%) Query: 1304 KSDYTELSLIRSELGKKNRNIPIRQLISRAKNSLLQLKPCFMMSPMSVANYLEPKDVKFD 1363 K E+ L+R +L K+ R K + + F ++ L + FD Sbjct: 311 KGIRKEIKLLRKDLRKRER--------KTVKEIISNSRVVFATLGGALDRLL--RKRTFD 360 Query: 1364 LVIMDESSQ-IKPEDALGVIARGKQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVAAVSQT 1422 LVI+DE++Q ++P+ + V+ GK+ ++ GDPKQLPPT D VS Sbjct: 361 LVIIDEAAQAMEPQCWIPVLK-GKKFILAGDPKQLPPTVLSDKAKRGGLQ------VSLL 413 Query: 1423 ESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYDN-----------SLIVFP----- 1466 E + + S L YR NE ++ SN FY+ L P Sbjct: 414 ERLAE-KFGNLSKILLNEQYRM-NEKIMNWSNEVFYNGQLKAASSVASHLLRDLPNVLAT 471 Query: 1467 ----SPYTSVDRYGVGFTHVKN--GVVVDQGNPEEARVIALAVKDHALRY---PEESLGV 1517 SP VD G + + + N EA+++ VK L + V Sbjct: 472 ESTKSPLVLVDTQGEKDEEKRGEEEELGSKYNEGEAKIVMEHVK--RLLEAGVQPSDIAV 529 Query: 1518 IAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFT 1577 I+ Q L+ + R +VE + ++ QG E+D + S Sbjct: 530 ISPYNAQVSLLREEDEEDFR---DVE--------------VGTVDGFQGREKDVVIFSLV 572 Query: 1578 YGPHEPGGRVFQRFGPINSDIGW----RRLNVLFTRSRR 1612 R + ++G+ RRLNV TR+RR Sbjct: 573 --------RSNDKG-----EVGFLGETRRLNVAITRARR 598 >gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]. Length = 935 Score = 53.5 bits (128), Expect = 6e-07 Identities = 36/173 (20%), Positives = 61/173 (35%), Gaps = 41/173 (23%) Query: 379 ASSNQNIEYKI------DEIEDIHQRCPL--------IDDSDSSQHSAVIDVINGKNLII 424 A + + + +ED + L + ++SQ +AV V+ +I Sbjct: 371 AVDEKKVSGYLYHKLLGHPVEDSSLKKLLPRRFSVPNLPKLNASQSNAVKHVLQRPLSLI 430 Query: 425 EGPPGTGKSQTITNII-AAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLG---------- 473 +GPPGTGK+ T I+ A H +L CA A++ + ++ K GL Sbjct: 431 QGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKTGLKVVRLCAKSRE 490 Query: 474 ------EFCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELK 520 F + + L L K D E++ +E K Sbjct: 491 DIESDVSFLSLHEQLRNMDKPELQKLLKLKDEGG----------ELSSSDEKK 533 Score = 50.4 bits (120), Expect = 4e-06 Identities = 89/399 (22%), Positives = 142/399 (35%), Gaps = 75/399 (18%) Query: 1250 LTEKPHLMHYSAVQFTAKQERFREYDKRLQFLQRQ-RIASVIGNQKIAQGISGGLKSDYT 1308 L EK H V+ AK E D L Q R QK+ + LK + Sbjct: 470 LAEKIHKTGLKVVRLCAKSREDIESDVSFLSLHEQLRNMDKPELQKLLK-----LKDEGG 524 Query: 1309 ELSLIRSELGKKNRNIPIRQLISRAKNSLLQLKPCFMMSPMSVANYLEPKDVKFDLVIMD 1368 ELS + R+L A+ LL + + + KF V++D Sbjct: 525 ELS--------SSDEKKYRKLKRAAEKELLNQADVICCTCVGAGD-RRLSKFKFRTVLID 575 Query: 1369 ESSQIKPEDALGVIARG-KQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVAAVSQTESILD 1427 E++Q + L + G KQ+V+VGD KQL P ++ A ++S+ + Sbjct: 576 EATQATEPECLIPLVLGAKQLVLVGDHKQLGPVIM----------CKKAATAGLSQSLFE 625 Query: 1428 ALLPLF-SMRRLQWHYRSLNENLIACSNYYFYDNSL-------------IVFPSPYTSVD 1473 L+ L RLQ YR ++ L + FY+ L + FP P Sbjct: 626 RLISLGIKPIRLQVQYR-MHPALSEFPSNMFYEGELQNGVTEIERSPLGVDFPWPQPDKP 684 Query: 1474 RYGVGFTHVKNGVVVDQG-----NPEEA----RVIALAVKDHALRYPEESLGVIAMNAKQ 1524 + F + N EA ++I +K +GVI Q Sbjct: 685 ---LFFYVCYGQEEISASGTSFLNRTEAANCEKIITKLLKSGV---KPSQIGVITPYEGQ 738 Query: 1525 RDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFTYGPHEPG 1584 R I +N + S + ++ + +++ QG E+D I +S Sbjct: 739 RSYI---VNYMQTNGSLHKDLYKEVE-------VASVDAFQGREKDFIILSCVR------ 782 Query: 1585 GRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYL 1623 Q G +N RRLNV TR++ + + + L Sbjct: 783 SNEHQGIGFLNDP---RRLNVALTRAKYGLVIVGNPKVL 818 >gnl|CDD|29956 cd00221, Vsr, Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.. Length = 115 Score = 48.8 bits (116), Expect = 1e-05 Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 25/107 (23%) Query: 1660 KQDSDFAVSVVNELEKTGFACDSQLGDMGFSIDVVVRDPNNPGHYLMGIECDGAMYN--- 1716 +D+ +V + L + G+ Q D+ D+VV PG Y + I DG ++ Sbjct: 15 SKDTKPERAVRSALWELGYRFRKQDKDLPGKPDIVV-----PG-YRLAIFVDGCFWHGHP 68 Query: 1717 --------------SAKSAR--DRDRLRQEVLERMGWRIRRIWSVDW 1747 K R +RDR Q LER+GWR+ R+W + Sbjct: 69 CHKRKPPPKNTEFWLEKIERNVERDRRVQAALERLGWRVLRVWECEL 115 >gnl|CDD|32680 COG2852, COG2852, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 129 Score = 41.1 bits (96), Expect = 0.003 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 3/61 (4%) Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELRELIS 1767 +E DG + + + D R LE G+ + R W+ + N D V+E I+ L E Sbjct: 69 VELDGGQH---EEREEYDAERDAFLESQGFTVLRFWNDEVLQNIDRVLEEILAVLEERRP 125 Query: 1768 Q 1768 Sbjct: 126 P 126 >gnl|CDD|37017 KOG1806, KOG1806, KOG1806, DEAD box containing helicases [Replication, recombination and repair]. Length = 1320 Score = 40.4 bits (94), Expect = 0.005 Identities = 76/353 (21%), Positives = 124/353 (35%), Gaps = 69/353 (19%) Query: 1294 KIAQGISGGLKSDYTELSLIR-SELGKKNRNIPIRQLISRAKNSLLQLKPCFMMSPMSVA 1352 A G L+ + +L R EL +R R L++ M+ A Sbjct: 928 DYATGCFRHLEYIFQQLEEFRAFEL--------LRSGEDRELYLLVKQAKIIAMTCTHAA 979 Query: 1353 ---NYLEPKDVKFDLVIMDESSQI------------KPEDALGVIARGKQIVVVGDPKQL 1397 L K+D ++M+ES+QI P+D R K+ +++GD QL Sbjct: 980 LRRGDLVKLGFKYDNLLMEESAQILEIETFIPLLLQNPQDGH---NRLKRWILIGDHHQL 1036 Query: 1398 PPT----RFFDHDNDQEDYDEEVAAVSQTESILDA-------LLPLFSMRRLQWHYRSLN 1446 PP F + N ++ + + L+A + L+ W Y L Sbjct: 1037 PPVVKNQAFQKYSNMEQSLFTRLVRLGVPIIDLNAQGRARASIASLY-----NWRYPLLG 1091 Query: 1447 ENLIACSNYYF-YDNSLIVFPSPYTSVDRY-GVGFTHVKNGVVVDQGNPEEARVIALAVK 1504 F Y N+ + + +V + G G T G + G E A +AL Sbjct: 1092 NLPHVSPLPRFQYANAGFAYEFQFINVPDFKGSGETEPSPGFYQNLGEAEYA--VALFQY 1149 Query: 1505 DHALRYPEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENV 1564 L YP + ++ Q+ LI IN+ C + + P + ++ Sbjct: 1150 MRLLGYPANKISILTTYNGQKSLIRDIINRRCSHNPFI----------GQPAKVTTVDKF 1199 Query: 1565 QGDERDRIFISFTYGPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVF 1617 QG + D I +S V R D+ RRL V +R+R + V Sbjct: 1200 QGQQNDFIILSL----------VRTREVGHLRDV--RRLVVAMSRARLGLYVL 1240 >gnl|CDD|113256 pfam04480, DUF559, Protein of unknown function (DUF559). Length = 109 Score = 38.9 bits (91), Expect = 0.012 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%) Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELR 1763 +E DG ++ + D R LE G+ + R W+ + NP+ V+E I+ EL Sbjct: 57 VELDGGQHDEQ---EEYDARRTAWLESQGFTVLRFWNDEVLKNPEGVLEEILLELE 109 >gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. Length = 103 Score = 38.4 bits (90), Expect = 0.017 Identities = 14/44 (31%), Positives = 24/44 (54%) Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452 Q A+ +++ K +I G+GK+ T +IA + KK+LF Sbjct: 8 QIEAIRNLLEKKRGLIVMATGSGKTLTAAKLIARLLKGKKKVLF 51 >gnl|CDD|29960 cd01038, Endonuclease_DUF559, Domain of unknown function, appears to be related to a diverse group of endonucleases.. Length = 108 Score = 38.3 bits (89), Expect = 0.019 Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 3/56 (5%) Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELR 1763 +E DG D R LE G+R+ R W+ + N + V+E I+ L Sbjct: 56 VELDGG---QHDEQIAYDAERDAWLEARGFRVLRFWNNEVLRNIEAVLEAILAALA 108 >gnl|CDD|36346 KOG1131, KOG1131, KOG1131, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription, Replication, recombination and repair]. Length = 755 Score = 34.2 bits (78), Expect = 0.31 Identities = 15/56 (26%), Positives = 31/56 (55%), Gaps = 4/56 (7%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGK----KILFCAQKMAAIEVVRHRLEK 469 + ++E P GTGK+ ++ ++I A LH K+++C++ + IE L++ Sbjct: 34 AKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR 89 >gnl|CDD|37012 KOG1801, KOG1801, KOG1801, tRNA-splicing endonuclease positive effector (SEN1) [RNA processing and modification]. Length = 827 Score = 33.9 bits (77), Expect = 0.41 Identities = 58/295 (19%), Positives = 87/295 (29%), Gaps = 50/295 (16%) Query: 1360 VKFDLVIMDESSQIK-PEDALGVIARGKQ-IVVVGDPKQLPPTRFFDHDNDQEDYDEEVA 1417 D V++DE++Q P + G Q ++VGD QLP T H + + Sbjct: 535 PPLDTVVIDEAAQKYEPSSLEPLQLAGYQHCILVGDLAQLPATV---HSSPAGCF----- 586 Query: 1418 AVSQTESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYD--------------NSLI 1463 S+ + L L ++ + + FY L Sbjct: 587 --KYMTSLFERLELAGHKTLLLTVQYRMHPEISRFPSKEFYGGRLKDVNNVSESNTVKLW 644 Query: 1464 VFPSPYTSVDRYGVGFTHVKNGVVVDQGNPEEARVIALAVKDH-----ALRYPEESLGVI 1518 + + V + + G N EE R + S+GVI Sbjct: 645 HSGETFGPYPFFNVHYGKERAGGGKSPVNNEEVRFVGAIYSRLYKVSQPQVSVPGSVGVI 704 Query: 1519 AMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFTY 1578 + Q + + +S D F QG ERD I IS Sbjct: 705 SPYKNQVKALRERFPEAYSLLLANNVDLS--VSTVDSF--------QGGERDIIIISTVR 754 Query: 1579 GPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDVVVDIDSKL 1633 E G I + RRLNV TR+R + L I + L Sbjct: 755 SIDE---------GSIGFECNLRRLNVALTRARTCFWLVGNEITLAPSCSIWASL 800 >gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function. Length = 178 Score = 33.4 bits (77), Expect = 0.52 Identities = 12/35 (34%), Positives = 18/35 (51%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452 +NL++ GPPG GK+ + A G +LF Sbjct: 46 QAENLLLLGPPGVGKTHLACALGHQACRAGYSVLF 80 >gnl|CDD|36207 KOG0989, KOG0989, KOG0989, Replication factor C, subunit RFC4 [Replication, recombination and repair]. Length = 346 Score = 33.4 bits (76), Expect = 0.58 Identities = 23/108 (21%), Positives = 42/108 (38%), Gaps = 22/108 (20%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL------FCAQKMAAIEVVRHRL---E 468 + + GPPGTGK+ T + A L+ +++ A I VVR ++ Sbjct: 56 ILPHYLFYGPPGTGKTSTA--LAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFA 113 Query: 469 KAGLGEFCLELHSHKVHKRAILDD-----------LRKRIDNRNIKTV 505 K + + + K ILD+ LR+ +++ + T Sbjct: 114 KLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTR 161 >gnl|CDD|36209 KOG0991, KOG0991, KOG0991, Replication factor C, subunit RFC2 [Replication, recombination and repair]. Length = 333 Score = 33.0 bits (75), Expect = 0.74 Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 8/79 (10%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKK----ILFCAQKMAAIEVVRHRLEKAGLG 473 N NLII GPPGTGK+ +I +A +L + A I+VVR++++ Sbjct: 47 NMPNLIISGPPGTGKTTSIL-CLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQK 105 Query: 474 EFCLELHSHKVHKRAILDD 492 + L HK+ ILD+ Sbjct: 106 KVTLPPGRHKI---IILDE 121 >gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.. Length = 165 Score = 32.8 bits (74), Expect = 0.90 Identities = 7/32 (21%), Positives = 16/32 (50%) Query: 421 NLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452 +++ GP G+GK+ + G K+++ Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVY 32 >gnl|CDD|38148 KOG2937, KOG2937, KOG2937, Decapping enzyme complex, predicted pyrophosphatase DCP2 [RNA processing and modification]. Length = 348 Score = 32.3 bits (73), Expect = 1.3 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%) Query: 1655 KTKTNKQDSDFAVSVVNELEKTGFACDSQLGDMGFSIDVVVRDPNNPGHYLMGIECD 1711 + K +K +SD ++ E+TGF QL D I+ +RD + G+ D Sbjct: 112 RGKISKDESDSDCAIREVTEETGFDYSKQLQDNEG-IETNIRDQLVRLFIINGVSED 167 >gnl|CDD|31392 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]. Length = 654 Score = 32.0 bits (72), Expect = 1.6 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 5/53 (9%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAA---AMLHGKKILFCAQKMAAIEVVRHRL 467 G+ L+IE P GTGK T+ ++ A A GKK++ + A E + Sbjct: 33 GGEGLLIEAPTGTGK--TLAYLLPALAYAREEGKKVIISTRTKALQEQLLEED 83 >gnl|CDD|31058 COG0714, COG0714, MoxR-like ATPases [General function prediction only]. Length = 329 Score = 32.0 bits (72), Expect = 1.6 Identities = 12/52 (23%), Positives = 29/52 (55%), Gaps = 1/52 (1%) Query: 412 AVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVV 463 A++ ++ G ++++EGPPG GK+ + +A A+ + C + +++ Sbjct: 36 ALLALLAGGHVLLEGPPGVGKT-LLARALARALGLPFVRIQCTPDLLPSDLL 86 >gnl|CDD|39016 KOG3812, KOG3812, KOG3812, L-type voltage-dependent Ca2+ channel, beta subunit [Inorganic ion transport and metabolism, Signal transduction mechanisms]. Length = 475 Score = 32.0 bits (72), Expect = 1.7 Identities = 30/131 (22%), Positives = 55/131 (41%), Gaps = 19/131 (14%) Query: 486 KRAILDDLRKRIDNR-NIKTVPQEIDVE------------ITRYEELKGQLNQYAQEINQ 532 ++A+ D L+ R D R +I V +I + I + L + EI + Sbjct: 195 QKALFDFLKHRFDGRISITRVTADISLAKRSVLNNPSKRAIIERSNTRSSLAEVQSEIER 254 Query: 533 IWKNTELSIHQILMGAARYRH-----NLPLDPVQLHVEGLSGENADRLLRSRLEDQIKAF 587 I++ S+ +++ A H L P+ ++++ S + RL+RSR + Q K Sbjct: 255 IFELAR-SLQLVVLDADTINHPAQLAKTSLAPIIVYIKVSSPKVLQRLIRSRGKSQSKHL 313 Query: 588 KDVIVEFHKQA 598 +V K A Sbjct: 314 NVQMVAADKLA 324 >gnl|CDD|73237 cd00820, PEPCK_HprK, Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting that these two phosphotransferases have related functions.. Length = 107 Score = 31.9 bits (72), Expect = 1.8 Identities = 10/34 (29%), Positives = 18/34 (52%) Query: 407 SSQHSAVIDVINGKNLIIEGPPGTGKSQTITNII 440 +S H ++DV ++I G G GK++ +I Sbjct: 3 TSLHGVLVDVYGKVGVLITGDSGIGKTELALELI 36 >gnl|CDD|37015 KOG1804, KOG1804, KOG1804, RNA helicase [RNA processing and modification]. Length = 775 Score = 31.5 bits (71), Expect = 2.2 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 2/47 (4%) Query: 423 IIEGPPGTGKSQTITNIIAAAMLHGKK--ILFCAQKMAAIEVVRHRL 467 I+ GPPGTGK++ IA IL CA A+ + HRL Sbjct: 330 IVFGPPGTGKTENYREAIAIVSFTSPHFYILVCAPSNASGKQPAHRL 376 >gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. Length = 168 Score = 31.4 bits (72), Expect = 2.3 Identities = 10/30 (33%), Positives = 15/30 (50%) Query: 421 NLIIEGPPGTGKSQTITNIIAAAMLHGKKI 450 + I GPPG GK+ + +I G K+ Sbjct: 1 RIFITGPPGVGKTTLVKKVIELLKSEGVKV 30 >gnl|CDD|31860 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]. Length = 858 Score = 31.3 bits (70), Expect = 2.3 Identities = 26/139 (18%), Positives = 47/139 (33%), Gaps = 16/139 (11%) Query: 389 IDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHGK 448 +DE + + D Q VID+ +L+I G G+GKS + +I + + Sbjct: 500 LDEFLERFPLGVIDLPKDIRQEPIVIDLAKAGHLLIAGATGSGKSVALNTMILSLLYTHS 559 Query: 449 K-------ILFCAQKMAAIEVVRHRLEKAGLGEFCLELHSHKVHKRAILDDLRKRIDNRN 501 I ++AA + + H + K L +L ++ R Sbjct: 560 PEEVRFYIIDPKMLELAAYDGLPHLGDPVV--------TDEKEKAEKALAELVAEMERRY 611 Query: 502 IKTVPQEIDVEITRYEELK 520 + + I Y E Sbjct: 612 KLFSEKGVRN-IEGYNEKI 629 >gnl|CDD|132846 cd07207, Pat_ExoU_VipD_like, ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2. ExoU, a 74-kDa enzyme, is a potent virulence factor of Pseudomonas aeruginosa. One of the pathogenic mechanisms of P. aeruginosa is to induce cytotoxicity by the injection of effector proteins (e.g. ExoU) using the type III secretion (T3S) system. ExoU is homologus to patatin and also has the conserved catalytic residues of mammalian calcium-independent (iPLA2) and cytosolic (cPLA2) PLA2. In vitro, ExoU cytotoxity is blocked by the inhibitor of cytosolic and Ca2-independent phospholipase A2 (cPLA2 and iPLA2) enzymes, suggesting that phospholipase A2 inhibitors may represent a novel mode of treatment for acute P. aeruginosa infections. ExoU requires eukaryotic superoxide dismutase as a cofactor and cleaves phosphatidylcholine and phosphatidylethanolamine in vitro. VipD, a 69-kDa cytosolic protein, belongs to the members of Legionella pneumophila family and is homologus to ExoU from Pseudomonas. Even though VipD shows high sequence similarity with several functional regions of ExoU (e.g. oxyanion hole, active site serine, active site aspartate), it has been shown to have no phospholipase activity. This family includes ExoU from Pseudomonas aeruginosa and VipD of Legionella pneumophila. Length = 194 Score = 31.5 bits (72), Expect = 2.4 Identities = 25/136 (18%), Positives = 45/136 (33%), Gaps = 26/136 (19%) Query: 162 GY--ADIEDLERAIKENKPLKPPHFQ----NNLSDNQI--QTAYFQDKLESILRLINEKS 213 GY ADI+D+ + K L P +L + ++ L +L+ S Sbjct: 47 GYSAADIKDILKETDFAKLLDSPVGLLFLLPSLFKEGGLYKGDALEEWLRELLKEKTGNS 106 Query: 214 QISIKET-----GTSILYIV-----LGFLEWYEIDDYDNPRLAPLFTIPVALEKRSSTSQ 263 + L +V G L + + + +PVA R+S S Sbjct: 107 FATSLLRDLDDDLGKDLKVVATDLTTGALVVFSAETTPD--------MPVAKAVRASMSI 158 Query: 264 PGLTQYHLRYTGEEII 279 P + + G+ + Sbjct: 159 PFVFKPVRLAKGDVYV 174 >gnl|CDD|29833 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.. Length = 149 Score = 31.4 bits (71), Expect = 2.4 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 7/70 (10%) Query: 410 HSAVIDVINGKNLIIEGPPGTGKSQTITNII-AAAMLHGKKILFCAQKM-----AAIEVV 463 H +++V G ++I GP G GKS+ +I L + ++ A E + Sbjct: 6 HGVLVEV-GGIGVLITGPSGIGKSELALELIKRGHRLVADDRVVVKREGGRLVGRAPEAL 64 Query: 464 RHRLEKAGLG 473 + +E GLG Sbjct: 65 KGLIEIRGLG 74 >gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 167 Score = 31.1 bits (71), Expect = 2.6 Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 7/37 (18%) Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAML 445 Q A+ ++ GK+++++ P G+GK+ A +L Sbjct: 4 QAEAIPAILEGKDVLVQAPTGSGKT-------LAFLL 33 >gnl|CDD|48371 cd02117, NifH_like, This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.. Length = 212 Score = 31.3 bits (71), Expect = 2.6 Identities = 14/32 (43%), Positives = 18/32 (56%) Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 + + I G G GKS T N+ AA GKK+L Sbjct: 1 RQIAIYGKGGIGKSTTSQNLSAALAEMGKKVL 32 >gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. Length = 207 Score = 31.3 bits (72), Expect = 2.7 Identities = 9/15 (60%), Positives = 13/15 (86%) Query: 419 GKNLIIEGPPGTGKS 433 G NL++ GPPG+GK+ Sbjct: 22 GHNLLMIGPPGSGKT 36 >gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]. Length = 260 Score = 30.8 bits (69), Expect = 3.2 Identities = 17/116 (14%), Positives = 41/116 (35%), Gaps = 15/116 (12%) Query: 419 GKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLE 478 G ++I GPPGTGK+ + G+ +L+ + + + E++ Sbjct: 23 GSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEESPEELLE-------------N 69 Query: 479 LHSHKVHKRAILDDLRKRIDNRNIKTVPQ--EIDVEITRYEELKGQLNQYAQEINQ 532 S ++ + I + + + + EEL ++ + ++ Sbjct: 70 ARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEKEGA 125 >gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]. Length = 254 Score = 30.7 bits (69), Expect = 3.4 Identities = 22/124 (17%), Positives = 44/124 (35%), Gaps = 7/124 (5%) Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF--CAQKMAAIEVVRHRLEKAGLGEF 475 G+NL++ GPPG GK+ I + G +LF ++ ++ Sbjct: 104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLE----- 158 Query: 476 CLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWK 535 L K I+DD+ ++ + ++ L N E ++++ Sbjct: 159 EKLLRELKKVDLLIIDDIGYEPFSQEEADLLFQLISRRYESRSLIITSNLSFGEWDELFG 218 Query: 536 NTEL 539 + L Sbjct: 219 DDAL 222 >gnl|CDD|177096 CHL00204, ycf1, Ycf1; Provisional. Length = 1832 Score = 30.8 bits (70), Expect = 3.7 Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 8/74 (10%) Query: 108 YDSDDEKKNYQVLQKVRDLIVEDIKTSNDLVDIREIEKKIEISLQKLTSIIQNYGYADIE 167 +S++E K ++ L D + I+EI KK+ KL ++E Sbjct: 558 INSEEEIKIFKFLFDAVITDPNDQTIIKKSIGIKEISKKVPRWSYKLID--------ELE 609 Query: 168 DLERAIKENKPLKP 181 LE +EN P Sbjct: 610 QLEGENEENVPSDH 623 >gnl|CDD|29370 cd00288, Pyruvate_Kinase, Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state. PK exists as several different isozymes, depending on organism and tissue type. In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung. PK forms a homotetramer, with each subunit containing three domains. The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer.. Length = 480 Score = 30.6 bits (69), Expect = 3.7 Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 8/107 (7%) Query: 69 TKKQAQAYGFADTGNHHTIDESTWIEKLGLSINYDLPIEYDSDDEKKNYQVLQKVRDLIV 128 K + N + + G + DLP + D + V Q V + Sbjct: 136 LSKDDDKTLVCEVLNGGVLGSRKGVNLPGTDV--DLPALSEKDKADLRFGVEQGVDMIFA 193 Query: 129 EDIKTSNDLVDIREI--EKKIEISLQKLTSIIQNY-GYADIEDLERA 172 ++ ++D+++IRE+ EK +I K+ + I+N G + +++ A Sbjct: 194 SFVRKASDVLEIREVLGEKGKDI---KIIAKIENQEGVNNFDEILEA 237 >gnl|CDD|30853 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]. Length = 696 Score = 30.9 bits (69), Expect = 3.9 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 3/40 (7%) Query: 1363 DLVIMDESSQIKPEDALGV---IARGKQIVVVGDPKQLPP 1399 DL+I+DE+S + A G+ I + ++++VGD QLP Sbjct: 409 DLLIIDEASMLDTSLAFGLLSAIGKLAKVILVGDVDQLPS 448 >gnl|CDD|144975 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli and the stage III sporulation protein E SpoIIIE which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer. Length = 202 Score = 30.8 bits (70), Expect = 4.0 Identities = 12/38 (31%), Positives = 21/38 (55%) Query: 406 DSSQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAA 443 D S + V D++ +L+I G G+GKS + +I + Sbjct: 25 DISGNPVVADLVKMPHLLIAGATGSGKSTFLNTLILSL 62 >gnl|CDD|32863 COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]. Length = 353 Score = 30.7 bits (69), Expect = 4.1 Identities = 12/25 (48%), Positives = 18/25 (72%) Query: 405 SDSSQHSAVIDVINGKNLIIEGPPG 429 SD+S SA+I+ I+GK +I + P G Sbjct: 168 SDASGDSAIIEPIDGKLVIHDNPYG 192 >gnl|CDD|30559 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]. Length = 655 Score = 30.5 bits (68), Expect = 4.1 Identities = 29/123 (23%), Positives = 47/123 (38%), Gaps = 7/123 (5%) Query: 408 SQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHG----KKILFCAQKMAAIEVV 463 + + +G L++ G G+GK++ +T IA + G ++IL A + Sbjct: 5 PEQREAVLHPDGPLLVLAGA-GSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEM 63 Query: 464 RHRLEKAGLGEFCLELHSHKVHKRA--ILDDLRKRIDNRNIKTVPQEIDVEITRYEELKG 521 R RL K L H A IL +R+ T+ D E L+ Sbjct: 64 RERLLKLLGLPAAEGLTVGTFHSFALRILRRHGERLGLNANFTILDSDDQLALIKELLRR 123 Query: 522 QLN 524 +LN Sbjct: 124 ELN 126 >gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein. IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter. Length = 370 Score = 30.4 bits (69), Expect = 4.5 Identities = 8/23 (34%), Positives = 16/23 (69%) Query: 423 IIEGPPGTGKSQTITNIIAAAML 445 ++ GP G GKSQ + N+++ ++ Sbjct: 91 VVYGPTGCGKSQLLRNLLSCQLI 113 >gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.. Length = 151 Score = 30.6 bits (69), Expect = 4.5 Identities = 13/33 (39%), Positives = 16/33 (48%) Query: 419 GKNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 KNL++ GPPGTGK+ I G L Sbjct: 19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFL 51 >gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]. Length = 845 Score = 30.3 bits (68), Expect = 4.7 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 2/43 (4%) Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQ--KMAAIEV 462 +II G G+GK+ + + L + C Q ++AA V Sbjct: 68 VIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSV 110 >gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Bacillus subtilis addA and Escherichia coli exodeoxyribonuclease V beta have large insertions near to the carboxy-terminus relative to other members of the family. Length = 494 Score = 30.4 bits (69), Expect = 4.8 Identities = 46/191 (24%), Positives = 75/191 (39%), Gaps = 38/191 (19%) Query: 417 INGKNLIIEGPPGTGKSQTITNIIAAAMLHG----KKIL---FCAQKMAAIEVVRHRLEK 469 + G L++ G GTGK++ +T IA +L G ++IL F AA E ++ R+ K Sbjct: 12 LGGPLLVLAGA-GTGKTRVLTERIAYLILEGGIDPEEILAVTF--TNKAARE-MKERILK 67 Query: 470 AGLGEFCLE------LHS--HKVHKRAI--LDDLRKR---IDNRNIKTVPQEIDVEITRY 516 LG+ HS ++ ++ + DL +D + + +EI ++ R Sbjct: 68 L-LGKAEASELNISTFHSFCLRILRKYANRIGDLLPNFSILDELDQLALLKEI-LKKDRL 125 Query: 517 EELKGQLNQYAQEINQI--WKNTELSIHQILMGAARYRHNLPLDPV----QLHVEGLSGE 570 + L + I KN LS ++ A Y Q + E L Sbjct: 126 DLDSKLLRPLLELKELISKAKNELLSPEELQ--QASYAATPRDKLAAEFYQEYQERLKEN 183 Query: 571 NA----DRLLR 577 NA D LL Sbjct: 184 NALDFDDLLLL 194 >gnl|CDD|143847 pfam00063, Myosin_head, Myosin head (motor domain). Length = 679 Score = 30.3 bits (69), Expect = 5.0 Identities = 20/102 (19%), Positives = 42/102 (41%), Gaps = 23/102 (22%) Query: 482 HKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTELSI 541 ++++ ++L +L+KR I T + + + Y+ +L Y +E ++ Sbjct: 8 TQLNETSVLHNLKKRYTGDLIYTYSGLVLISVNPYK----RLPIYTEEPIGEYR------ 57 Query: 542 HQILMGAARYRHNLPLDPVQLHVEGLSGENADRLLRSRLEDQ 583 + R LP P H+ L+ + A R + E+Q Sbjct: 58 -------GKRRGELP--P---HIFALA-DRAYRHMLRDKENQ 86 >gnl|CDD|28927 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.. Length = 144 Score = 30.1 bits (67), Expect = 5.2 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 2/81 (2%) Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLH--GKKILFCAQKMAAIEVVRHRLEKAGLGEFCL 477 +++++ P G+GK+ I + G ++L A V RL++ + Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60 Query: 478 ELHSHKVHKRAILDDLRKRID 498 + L + D Sbjct: 61 GYLIGGTSIKQQEKLLSGKTD 81 >gnl|CDD|36134 KOG0916, KOG0916, KOG0916, 1,3-beta-glucan synthase/callose synthase catalytic subunit [Cell wall/membrane/envelope biogenesis]. Length = 1679 Score = 30.3 bits (68), Expect = 5.4 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%) Query: 827 SVLEELFERLDSLKILQESLDDVFNMKKLPD 857 ++ L +R+ S KIL L+ F K LP Sbjct: 715 NIFSRLPKRIYS-KILATDLEIEFKPKVLPS 744 >gnl|CDD|30951 COG0606, COG0606, Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]. Length = 490 Score = 30.2 bits (68), Expect = 5.7 Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 11/60 (18%) Query: 393 EDIHQRCPLIDDSD-SSQHSA----VIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHG 447 E I D D Q A I G NL++ GPPGTGK+ + A+ L G Sbjct: 167 EVIESFSLAPDFKDVKGQEQAKRALEIAAAGGHNLLLVGPPGTGKT------MLASRLPG 220 >gnl|CDD|38888 KOG3684, KOG3684, KOG3684, Ca2+-activated K+ channel proteins (intermediate/small conductance classes) [Inorganic ion transport and metabolism]. Length = 489 Score = 29.9 bits (67), Expect = 6.5 Identities = 22/110 (20%), Positives = 46/110 (41%), Gaps = 11/110 (10%) Query: 907 LPNAYQFAVEKEKLEKRNFGNTLGEHYRGLSTDIVALKNIREWYRKVHQIWKDNSSLDDA 966 L + + + K + L +H R I ++++ RK+ + + NS +D A Sbjct: 370 LQETWLIYKHTKLVSKGDQAR-LRKHQRKFLQAIHQFRSVKWEQRKLSE--QANSLVDLA 426 Query: 967 LINGFLMLDSQLFKRIQKLHC--DELSKKITKVFGRIQELEQFLPKQKEL 1014 + ++ +Q+LH +EL K+I + +++ L L L Sbjct: 427 ------KTQNDMYDLLQELHSRQEELEKQIDTLESKLEALTASLSSLPGL 470 >gnl|CDD|48369 cd02040, NifH, NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.. Length = 270 Score = 29.8 bits (67), Expect = 6.7 Identities = 13/32 (40%), Positives = 18/32 (56%) Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 + + I G G GKS T N+ AA GKK++ Sbjct: 2 RQIAIYGKGGIGKSTTTQNLSAALAEMGKKVM 33 >gnl|CDD|73296 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.. Length = 147 Score = 29.7 bits (67), Expect = 6.9 Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 10/55 (18%) Query: 424 IEGPPGTGKSQTITNIIAAAM---------LHGKKILFCAQKMAAIEVVRHRLEK 469 I+GP G+GKS T+ ++A + + +++ A ++AAI VR L++ Sbjct: 4 IDGPAGSGKS-TVAKLLAKKLGLPYLDTGGIRTEEVGKLASEVAAIPEVRKALDE 57 >gnl|CDD|35549 KOG0328, KOG0328, KOG0328, Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]. Length = 400 Score = 29.9 bits (67), Expect = 7.2 Identities = 9/29 (31%), Positives = 18/29 (62%) Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTIT 437 Q A+ ++ G+++I + GTGK+ T + Sbjct: 54 QQRAIPQILKGRDVIAQAQSGTGKTATFS 82 >gnl|CDD|31498 COG1307, DegV, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 282 Score = 29.8 bits (67), Expect = 7.2 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 4/75 (5%) Query: 1075 EESLIKKFFGEEIKLSVFDSNTKESNKSLAVINSTLEFAHSIRERVLFDELIQGINHIDD 1134 + + + E K+ V DS + S+ + LE A + F+E+++ + I + Sbjct: 98 QSAQLAAELVEGAKVHVIDS----KSVSMGLGFLVLEAAELAKAGKSFEEILKKLEEIRE 153 Query: 1135 HTIYNSFIKDLKNLR 1149 T + DL NL Sbjct: 154 KTKAYFVVDDLDNLV 168 >gnl|CDD|37153 KOG1942, KOG1942, KOG1942, DNA helicase, TBP-interacting protein [Replication, recombination and repair]. Length = 456 Score = 29.5 bits (66), Expect = 7.6 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 14/64 (21%) Query: 413 VIDVIN-----GKNLIIEGPPGTGKSQTITNIIAAAMLH--GKKILFCAQKMAAIEVVRH 465 ++D+I G+ +++ GPPGTGK+ +A A+ G K+ FC M EV + Sbjct: 53 IVDLIKSKKMAGRAVLLAGPPGTGKTA-----LALAISQELGPKVPFCP--MVGSEVYSN 105 Query: 466 RLEK 469 ++K Sbjct: 106 EVKK 109 >gnl|CDD|48362 cd02032, Bchl_like, This family of proteins contains bchL and chlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.. Length = 267 Score = 29.5 bits (66), Expect = 8.2 Identities = 13/30 (43%), Positives = 17/30 (56%) Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451 L + G G GKS T +N+ A GKK+L Sbjct: 3 LAVYGKGGIGKSTTSSNLSVALAKRGKKVL 32 >gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing and modification]. Length = 674 Score = 29.5 bits (66), Expect = 8.2 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 2/51 (3%) Query: 416 VINGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQ--KMAAIEVVR 464 V + + LI+ G G+GKS I +A A + C Q ++AA+ + + Sbjct: 63 VEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAK 113 >gnl|CDD|110585 pfam01591, 6PF2K, 6-phosphofructo-2-kinase. This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyses both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. This enzyme contains a P-loop motif. Length = 223 Score = 29.6 bits (67), Expect = 8.4 Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 13/90 (14%) Query: 1059 FSAKLHKIREKNIVLAEESLIKKFFGEEIKLSVFDS--NTKESNKSLAVINSTLEFAHSI 1116 + + KIRE+ + A + ++ E ++++FD+ T+E K++ L+FA Sbjct: 69 DNTEAMKIREQCALAALKDVLAYLNEESGQVAIFDATNTTRERRKNI------LDFAEEN 122 Query: 1117 RERVLFDELIQGINHIDDHTIYNSFIKDLK 1146 +V F E I DD I IK +K Sbjct: 123 GLKVFFLESI-----CDDPEIIARNIKLVK 147 >gnl|CDD|31417 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein [Transcription]. Length = 450 Score = 29.5 bits (66), Expect = 9.9 Identities = 26/116 (22%), Positives = 46/116 (39%), Gaps = 24/116 (20%) Query: 417 INGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFC 476 + G+ ++I GPPGTGK+ + A G+ + F A ++ E+ ++K Sbjct: 63 MAGRGILIVGPPGTGKTAL---AMGIARELGEDVPFVA--ISGSEIYSLEVKKT------ 111 Query: 477 LELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEIT--RYEELKGQLNQYAQEI 530 A+ LR+ I R IK + + E+ + LN Y + Sbjct: 112 ----------EALTQALRRAIGVR-IKETREVYEGEVVELEIRRARNPLNPYGKVP 156 >gnl|CDD|35520 KOG0299, KOG0299, KOG0299, U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]. Length = 479 Score = 29.2 bits (65), Expect = 9.9 Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 4/94 (4%) Query: 1651 EHSLKTKTNKQDSDFAVSVVNELEKTGFACDSQLGDMGFSIDVVVRDPNNPGHYLMGIEC 1710 E + K N+ D + A + ++ E+ A + + D + YL I Sbjct: 29 EEEAERKKNRDDDEDAEEIESDEEENSLAGEEEEEDEFEEETAGEKRLRLAEEYLDEIRE 88 Query: 1711 DGAMYNSAKSARDR---DRLRQEVLERMGWRIRR 1741 A D RL+++VLE+ G R+RR Sbjct: 89 IEEDNFDADDLDDELVASRLKEDVLEQSG-RVRR 121 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.136 0.397 Gapped Lambda K H 0.267 0.0868 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 21,966,357 Number of extensions: 1226416 Number of successful extensions: 3701 Number of sequences better than 10.0: 1 Number of HSP's gapped: 3685 Number of HSP's successfully gapped: 91 Length of query: 1775 Length of database: 6,263,737 Length adjustment: 108 Effective length of query: 1667 Effective length of database: 3,929,965 Effective search space: 6551251655 Effective search space used: 6551251655 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: 65 (28.6 bits)