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)