RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780129|ref|YP_003064542.1| hypothetical protein
CLIBASIA_00040 [Candidatus Liberibacter asiaticus str. psy62]
(220 letters)
>gnl|CDD|143942 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5),
DNA recombination (e.g., RAD54), and chromatin unwinding
(e.g., ISWI) as well as a variety of other proteins with
little functional information (e.g., lodestar, ETL1).
Length = 295
Score = 75.4 bits (186), Expect = 1e-14
Identities = 59/201 (29%), Positives = 93/201 (46%), Gaps = 25/201 (12%)
Query: 8 HQIVMVNWLLS----HDRCALWASMGSGKTVSVLFALSTIKILDPR--PVLIIAPLRVAQ 61
+Q+ VNWL+S L MG GKT+ + L+ +K L P P L++ PL
Sbjct: 1 YQLEGVNWLISLYNNGLGGILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLSTLD 60
Query: 62 YVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLY-----IINFENIPWLVKMKLD 116
W +E E+W D+ + G R + L I ++E I K +L
Sbjct: 61 N-WLNEFEKW--APDLNIVVYYGDGDSRSELLRNVLRTGKFDVLITSYEYIR-RDKDELH 116
Query: 117 HWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLWGQI 176
++ +++DE ++K+ ++ K + AL + K + LTGTP N L +LW +
Sbjct: 117 KANWRYVILDEGHRIKNAKS----KLSLALKSL---KTNNRLLLTGTPIQNNLAELWSLL 169
Query: 177 WFLDKGKRLGLSFKSFVERWF 197
FL G G SFK F ++WF
Sbjct: 170 NFLRPG-IFG-SFKEF-DKWF 187
>gnl|CDD|30899 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 72.1 bits (175), Expect = 1e-13
Identities = 55/226 (24%), Positives = 96/226 (42%), Gaps = 28/226 (12%)
Query: 5 LKPHQIVMVNWLLS-----HDRCALWASMGSGKTVSVLFALSTIKILDPR---PVLIIAP 56
L+P+Q+ VNWL L MG GKTV + L ++ P LI+ P
Sbjct: 339 LRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVP 398
Query: 57 LRVAQYVWKDEVERWSAFSDMTVS-----SLIGSERQRIKALNTPAHLYIINF--ENIPW 109
+ WK E E+++ + + S + +R+ ++ L + I +
Sbjct: 399 ASLL-SNWKREFEKFAPDLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYEL 457
Query: 110 LVKMKLDHW-----DFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTP 164
L + +DH ++ +V+DE+ ++K+ ++ + +AL F K ++LTGTP
Sbjct: 458 LRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQS----SEGKALQ---FLKALNRLDLTGTP 510
Query: 165 SPNGLIDLWGQIWFLDKGKRLGLSFKSFVERWFHTQQVGSSIGAVK 210
N L +LW + LG SF F + Q IG ++
Sbjct: 511 LENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLE 556
>gnl|CDD|35606 KOG0385, KOG0385, KOG0385, Chromatin remodeling complex WSTF-ISWI,
small subunit [Transcription].
Length = 971
Score = 63.9 bits (155), Expect = 4e-11
Identities = 51/187 (27%), Positives = 87/187 (46%), Gaps = 22/187 (11%)
Query: 4 VLKPHQIVMVNWLLS----HDRCALWASMGSGKTVSVLFALSTIKIL--DPRPVLIIAPL 57
L+ +Q+ +NWL+S L MG GKT+ + L +K P P L+IAP
Sbjct: 167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPK 226
Query: 58 RVAQYVWKDEVERWSAFSDMTVSSLIGSERQRIKA-----LNTPAHLYIINFENIPWLVK 112
W +E +R++ + V G + +R L + I ++E I K
Sbjct: 227 STLDN-WMNEFKRFT--PSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYE-IAIKDK 282
Query: 113 MKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDL 172
L +++ +V+DE+ ++K+ + +K ++ L + F R + LTGTP N L +L
Sbjct: 283 SFLKKFNWRYLVIDEAHRIKN----EKSKLSKILRE--FKTDNRLL-LTGTPLQNNLHEL 335
Query: 173 WGQIWFL 179
W + FL
Sbjct: 336 WALLNFL 342
>gnl|CDD|36218 KOG1000, KOG1000, KOG1000, Chromatin remodeling protein
HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure
and dynamics].
Length = 689
Score = 63.1 bits (153), Expect = 6e-11
Identities = 51/200 (25%), Positives = 89/200 (44%), Gaps = 14/200 (7%)
Query: 5 LKPHQIVMVNWLLSHD-RCALWASMGSGKTVSVLFALSTIKILDPRPVLIIAPLRVAQYV 63
L P Q V + L R L MG GKT+ L A++ + P+LI+ P V ++
Sbjct: 199 LLPFQREGVIFALERGGRILLADEMGLGKTIQAL-AIARYYRAE-WPLLIVCPASV-RFT 255
Query: 64 WKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATI 123
W + R+ + ++ + + T + I+++E + L + L + +
Sbjct: 256 WAKALNRF--LPSIHPIFVVDKSSDPLPDVCTSNTVAIVSYEQLSLLHDI-LKKEKYRVV 312
Query: 124 VVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLWGQIWFLDKGK 183
+ DES LK +T K+T+A + K I L+GTP+ + +L+ QI +D
Sbjct: 313 IFDESHMLKDSKT----KRTKAATDLL-KVAKHVILLSGTPAVSRPSELYTQIRAVD--H 365
Query: 184 RLGLSFKSFVERWFHTQQVG 203
L +F F R+ +QV
Sbjct: 366 TLFPNFHEFAIRYCDGKQVR 385
>gnl|CDD|35608 KOG0387, KOG0387, KOG0387, Transcription-coupled repair protein
CSB/RAD26 (contains SNF2 family DNA-dependent ATPase
domain) [Transcription, Replication, recombination and
repair].
Length = 923
Score = 60.4 bits (146), Expect = 4e-10
Identities = 48/199 (24%), Positives = 79/199 (39%), Gaps = 30/199 (15%)
Query: 5 LKPHQIVMVNWL--LSHDRCA--LWASMGSGKTVSVLFALSTI--KILDPRPVLIIAPLR 58
L P+Q V WL L R L MG GKT+ ++ L+ + +P LI+ P
Sbjct: 206 LFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPAT 265
Query: 59 VAQYVWKDEVERWSAFSDMTV-------------SSLIGSERQRIKALNTPAHLYIINFE 105
+ W E + W + + S ++ I+ + T + I ++
Sbjct: 266 IIHQ-WMKEFQTWWPPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYD 324
Query: 106 NIPWLVKMKLDH-WDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTP 164
L WD+ ++DE ++++ +K + A K V R I L+GTP
Sbjct: 325 GFRIQGDDLLGILWDYV--ILDEGHRIRN----PNSKISLACKK--IRTVHRII-LSGTP 375
Query: 165 SPNGLIDLWGQIWFLDKGK 183
N L +LW F+ GK
Sbjct: 376 IQNNLTELWSLFDFVFPGK 394
>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 = 57.0 bits (137), Expect = 4e-09
Identities = 36/147 (24%), Positives = 62/147 (42%), Gaps = 9/147 (6%)
Query: 22 CALWASMGSGKT-VSVLFALSTIKILDPRPVLIIAPLRVAQYVWKDEVERWSAFSDMTVS 80
L A GSGKT ++L L + L VL++AP R E + + V
Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELA-NQVAERLKELFGEGIKVG 61
Query: 81 SLIG--SERQRIKALNTPAHLYIINFEN-IPWLVKMKLDHWDFATIVVDESTKLKSFRTH 137
LIG S +Q+ K L+ + + + L ++KL +++DE+ +L +
Sbjct: 62 YLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLN---- 117
Query: 138 QGTKQTRALGKVAFSKVKRFIELTGTP 164
QG + K ++ + L+ TP
Sbjct: 118 QGFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|35610 KOG0389, KOG0389, KOG0389, SNF2 family DNA-dependent ATPase
[Chromatin structure and dynamics].
Length = 941
Score = 55.7 bits (134), Expect = 1e-08
Identities = 52/195 (26%), Positives = 88/195 (45%), Gaps = 33/195 (16%)
Query: 3 LVLKPHQIVMVNWL-LSHDR---CALWASMGSGKTVSVLFALSTIK-ILDPRPVLIIAPL 57
+ LK +Q+V VNWL L + + L MG GKT+ V+ L+ +K I +P P L++ P
Sbjct: 398 IQLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPS 457
Query: 58 RVAQYVWKDEVERWSAFSDMTVSSLIGSE------RQRIKA-------LNTPAHLYIINF 104
+ W E +W + V GS+ R+RIK L T +L +
Sbjct: 458 STLEN-WLREFAKWC--PSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSK 514
Query: 105 ENIPWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTP 164
++ + L + F ++ DE LK+ + +++ + L + + LTGTP
Sbjct: 515 DD-----RSFLKNQKFNYVIYDEGHMLKN----RTSERYKHLMSI---NANFRLLLTGTP 562
Query: 165 SPNGLIDLWGQIWFL 179
N L +L + F+
Sbjct: 563 LQNNLKELISLLAFV 577
>gnl|CDD|35605 KOG0384, KOG0384, KOG0384, Chromodomain-helicase DNA-binding
protein [Transcription].
Length = 1373
Score = 53.1 bits (127), Expect = 6e-08
Identities = 52/196 (26%), Positives = 86/196 (43%), Gaps = 29/196 (14%)
Query: 5 LKPHQIVMVNWLL----SHDRCALWASMGSGKTVSVLFALSTIK--ILDPRPVLIIAPLR 58
L+ +Q+ +NWLL + C L MG GKTV + LS + + P L++ PL
Sbjct: 371 LRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLS 430
Query: 59 VAQYVWKDEVERWSAFSDMTVSSLIGSERQR--------IKALNTPA---HLYIINFENI 107
W+ E E W+ DM V G+ R + NT + + +E +
Sbjct: 431 TIT-AWEREFETWT---DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIV 486
Query: 108 PWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPN 167
K +L + ++VDE+ +LK+ +++ + K+ + +TGTP N
Sbjct: 487 -LKDKAELSKIPWRYLLVDEAHRLKN-------DESKLYESLNQFKMNHRLLITGTPLQN 538
Query: 168 GLIDLWGQIWFLDKGK 183
L +LW + FL GK
Sbjct: 539 SLKELWSLLHFLMPGK 554
>gnl|CDD|36233 KOG1015, KOG1015, KOG1015, Transcription regulator XNP/ATRX,
DEAD-box superfamily [Transcription].
Length = 1567
Score = 50.9 bits (121), Expect = 3e-07
Identities = 62/231 (26%), Positives = 96/231 (41%), Gaps = 49/231 (21%)
Query: 5 LKPHQIVMVNWLL-----SHDR--------CALWASMGSGKTVSVLFALSTIKI---LDP 48
LKPHQ+ V ++ S R C L MG GKT+ V+ L T+ + L
Sbjct: 669 LKPHQVDGVQFMWDCCCESLKRTKKSPGSGCILAHCMGLGKTLQVVTFLHTVLLCDKLGF 728
Query: 49 RPVLIIAPLRVAQYVWKDEVERW----SAFSDMTVSSLIGSER--QRIKALN---TPAHL 99
+ L++ PL A W +E E+W + VS L +R +R L +
Sbjct: 729 KTALVVCPLNTALN-WMNEFEKWMEGLEDDEKLEVSELATVKRPEERSYMLQRWQEDGGV 787
Query: 100 YIINFENIPWL-----VKMKLDHWDFAT---------IVVDESTKLKSFRTHQGTKQTRA 145
II ++ L VK + F +V DE LK+ + + ++A
Sbjct: 788 MIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKN----EKSAVSKA 843
Query: 146 LGKVAFSKVKRFIELTGTPSPNGLIDLWGQIWFLDKGKRLGLSFKSFVERW 196
+ + + KR I LTGTP N L++ + F+ + LG S K F R+
Sbjct: 844 MNSI---RTKRRIILTGTPLQNNLMEYHCMVNFVKEN-LLG-SIKEFRNRF 889
>gnl|CDD|35613 KOG0392, KOG0392, KOG0392, SNF2 family DNA-dependent ATPase
domain-containing protein [Transcription].
Length = 1549
Score = 50.4 bits (120), Expect = 4e-07
Identities = 45/193 (23%), Positives = 85/193 (44%), Gaps = 27/193 (13%)
Query: 5 LKPHQIVMVNWLLSHDRCALWA----SMGSGKTVSVLFAL--------STIKILDPRPVL 52
L+ +Q VNWL ++ L MG GKT+ + L S + P L
Sbjct: 976 LRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSL 1035
Query: 53 IIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLYIINFENIPWLVK 112
I+ P + + WK EV+++ F + +ER+ ++ A++ + +++ +V+
Sbjct: 1036 IVCPSTLTGH-WKSEVKKFFPFLKVLQYVGPPAERRELRDQYKNANIIVTSYD----VVR 1090
Query: 113 MKLDHW---DFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGL 169
+D+ D+ V+DE +K+ +T+ V + + L+GTP N +
Sbjct: 1091 NDVDYLIKIDWNYCVLDEGHVIKN-------SKTKLTKAVKQLRANHRLILSGTPIQNNV 1143
Query: 170 IDLWGQIWFLDKG 182
++LW FL G
Sbjct: 1144 LELWSLFDFLMPG 1156
>gnl|CDD|39640 KOG4439, KOG4439, KOG4439, RNA polymerase II transcription
termination factor TTF2/lodestar, DEAD-box superfamily
[Transcription, Replication, recombination and repair].
Length = 901
Score = 48.6 bits (115), Expect = 1e-06
Identities = 44/201 (21%), Positives = 76/201 (37%), Gaps = 36/201 (17%)
Query: 5 LKPHQIVMVNWLL-----SHDRCALWASMGSGKTVSVLFALSTIKIL---------DPRP 50
L PHQ + WLL L MG GKT+S++ + K
Sbjct: 326 LMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASK 385
Query: 51 VLIIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAH-LYIINFENIPW 109
LII P + + W+ EV R + ++V G ++ I A + + I + +
Sbjct: 386 TLIICPASLI-HQWEAEVARRLEQNALSVYLYHGPNKREISAKELRKYDVVITTYNLVAN 444
Query: 110 LVKMKLD-----------HWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFI 158
+L+ W + +++DE+ +++ T + K +
Sbjct: 445 KPDDELEEGKNSSPLARIAW--SRVILDEAHNIRNSNTQCSKAVCKLSAKSRWC------ 496
Query: 159 ELTGTPSPNGLIDLWGQIWFL 179
LTGTP N L D++ + FL
Sbjct: 497 -LTGTPIQNNLWDVYSLLRFL 516
>gnl|CDD|35612 KOG0391, KOG0391, KOG0391, SNF2 family DNA-dependent ATPase
[General function prediction only].
Length = 1958
Score = 47.8 bits (113), Expect = 2e-06
Identities = 50/187 (26%), Positives = 88/187 (47%), Gaps = 24/187 (12%)
Query: 5 LKPHQIVMVNWLLS----HDRCALWASMGSGKTVSV--LFALSTIKILDPRPVLIIAPLR 58
L+ +Q + ++WL + + L MG GKT+ L A + + P LI+ P
Sbjct: 616 LREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTS 675
Query: 59 VAQYVWKDEVERWSAFSDMTVSSLIGSERQRI---KALNTPA--HLYIINFENIPW-LVK 112
V W+ E++RW + + + GS ++R + P H+ I +++ + L
Sbjct: 676 VI-LNWEMELKRWCP--GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA 732
Query: 113 MKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDL 172
K W + +V+DE+ +K+F K R + F+ +R + LTGTP N L++L
Sbjct: 733 FKRKRWQY--LVLDEAQNIKNF------KSQRWQALLNFNSQRRLL-LTGTPLQNSLMEL 783
Query: 173 WGQIWFL 179
W + FL
Sbjct: 784 WSLMHFL 790
>gnl|CDD|35607 KOG0386, KOG0386, KOG0386, Chromatin remodeling complex SWI/SNF,
component SWI2 and related ATPases (DNA/RNA helicase
superfamily) [Chromatin structure and dynamics,
Transcription].
Length = 1157
Score = 47.4 bits (112), Expect = 3e-06
Identities = 56/221 (25%), Positives = 87/221 (39%), Gaps = 39/221 (17%)
Query: 5 LKPHQIVMVNWLLS----HDRCALWASMGSGKTVSVLFALSTI---KILDPRPVLIIAPL 57
LK +Q+ + W++S + L MG GKT+ + +L T P LII PL
Sbjct: 395 LKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTI-SLITYLMEHKQMQGPFLIIVPL 453
Query: 58 RVAQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHL----------YIINFENI 107
W E +W+ + G+ +QR H YII
Sbjct: 454 STLV-NWSSEFPKWA--PSVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK---- 506
Query: 108 PWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPN 167
K L + +++DE ++K+ K T L + +R + LTGTP N
Sbjct: 507 ---DKALLSKISWKYMIIDEGHRMKN---AIC-KLTDTLN--THYRAQRRLLLTGTPLQN 557
Query: 168 GLIDLWGQIWFLDKGKRLGLSFKSFVERWFHT--QQVGSSI 206
L +LW + FL + S K+F E+WF+ G +
Sbjct: 558 NLPELWALLNFLL--PNIFNSCKAF-EQWFNQPFANTGEKV 595
>gnl|CDD|35609 KOG0388, KOG0388, KOG0388, SNF2 family DNA-dependent ATPase
[Replication, recombination and repair].
Length = 1185
Score = 45.5 bits (107), Expect = 1e-05
Identities = 51/196 (26%), Positives = 90/196 (45%), Gaps = 36/196 (18%)
Query: 5 LKPHQIVMVNWLLS-HDRC---ALWASMGSGKTV---SVLFALSTIKILDPRPVLIIAPL 57
LK +Q+ +NWL++ +D+ L MG GKTV SVL L+ + P L++ P
Sbjct: 568 LKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQSISVLAHLAETHNI-WGPFLVVTPA 626
Query: 58 RVAQYVWKDEVER----------WSAFSDMTVSSLIGSERQRIKALNTPAHLYIINFENI 107
W E+ R W + S+ + R+ + N P H+ I +++ +
Sbjct: 627 STLHN-WAQEISRFLPSFKVLPYWGSPSERKILRKF-WNRKNMYRRNAPFHVVITSYQLV 684
Query: 108 ----PWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGT 163
+L K+K W + +++DE+ +KS + +R ++F R + LTGT
Sbjct: 685 VTDEKYLQKVK---WQY--MILDEAQAIKS------SSSSRWKTLLSFKCRNRLL-LTGT 732
Query: 164 PSPNGLIDLWGQIWFL 179
P N + +LW + F+
Sbjct: 733 PIQNSMQELWALLHFI 748
>gnl|CDD|35611 KOG0390, KOG0390, KOG0390, DNA repair protein, SNF2 family
[Replication, recombination and repair].
Length = 776
Score = 42.7 bits (100), Expect = 7e-05
Identities = 42/191 (21%), Positives = 71/191 (37%), Gaps = 34/191 (17%)
Query: 4 VLKPHQIVMVNWL---LSHDR-------CALWASMGSGKTVSVLFALSTIKILDPRPV-- 51
+L+PHQ +L L+ C + G GKT+ + + T+ P+
Sbjct: 238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPL 297
Query: 52 ----LIIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLY------- 100
L++AP + WK E +W + +++ L + L
Sbjct: 298 INKPLVVAPSSLV-NNWKKEFGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTP 356
Query: 101 --IINFENIPWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFI 158
II++E + L +V DE +LK+ + +AL + K R +
Sbjct: 357 VLIISYETASDYCRKILLI-RPGLLVCDEGHRLKN----SDSLTLKALSSL---KTPRRV 408
Query: 159 ELTGTPSPNGL 169
LTGTP N L
Sbjct: 409 LLTGTPIQNDL 419
>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 = 42.2 bits (100), Expect = 1e-04
Identities = 28/128 (21%), Positives = 54/128 (42%), Gaps = 9/128 (7%)
Query: 7 PHQIVMVNWLLSHDRCALWASMGSGKT-VSVLFALSTIKILDPRP-VLIIAPLR--VAQY 62
P Q + +L + A GSGKT +L AL + P L++AP R Q
Sbjct: 2 PIQAEAIPAILEGKDVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQI 61
Query: 63 VWKDEVERWSAFSDMTVSSLIG--SERQRIKALNTPAHLYIINFENIPWLVKMKLDHWD- 119
+E+++ + + V+ L G S +++++ L + + + L++
Sbjct: 62 Y--EELKKLGKYLGLKVALLYGGDSPKEQLRKLKKGPDILVGTPGRLLDLLERGGLLLKN 119
Query: 120 FATIVVDE 127
+V+DE
Sbjct: 120 LKLLVLDE 127
>gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 41.2 bits (96), Expect = 2e-04
Identities = 23/132 (17%), Positives = 51/132 (38%), Gaps = 15/132 (11%)
Query: 1 MHLVLKPHQI----VMVNWLLSHDRCALWASMGSGKTVSVLFALSTIKILDPRPVLIIAP 56
L+P+Q +V + R + G+GKTV A++ +K R L++ P
Sbjct: 33 FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELK----RSTLVLVP 88
Query: 57 LRVAQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLYIINFENIPWLVKMK-L 115
+ W + ++++ + G + ++ PA + + + + +
Sbjct: 89 TKELLDQWAEALKKF--LLLNDEIGIYGGGEKELE----PAKVTVATVQTLARRQLLDEF 142
Query: 116 DHWDFATIVVDE 127
+F I+ DE
Sbjct: 143 LGNEFGLIIFDE 154
>gnl|CDD|36234 KOG1016, KOG1016, KOG1016, Predicted DNA helicase, DEAD-box
superfamily [General function prediction only].
Length = 1387
Score = 37.0 bits (85), Expect = 0.004
Identities = 61/259 (23%), Positives = 94/259 (36%), Gaps = 76/259 (29%)
Query: 4 VLKPHQIVMVNWLL-----SHDR--------CALWASMGSGKTVSVL-FALSTIKILDPR 49
VLKPHQI + +L S R C L SMG GKT+ V+ F+ ++ +
Sbjct: 254 VLKPHQIGGIRFLYDNTIESLGRYKKSSGFGCILAHSMGLGKTLQVISFSDIFLRHTKAK 313
Query: 50 PVLIIAPLRVAQYVWKDEVERW--SAFSDMTVSS------LIGSER----QRIKALNTPA 97
VL+I P+ Q W E W FSD V L+ QR K +
Sbjct: 314 TVLVIVPINTLQN-WLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVKTFDQRAKVIEQWV 372
Query: 98 H---LYIINFENIPWLVKMKL--------------------DHWDFAT------------ 122
+ ++ +E L+ L D D
Sbjct: 373 QTGGVLLVGYEMFRLLILKTLPKKGRPKKTLKRISSGFIKDDSEDQRQEAYSLIRSALLE 432
Query: 123 -----IVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLWGQIW 177
++ DE ++K+ AL + + +R I LTG P N L++ W +
Sbjct: 433 PGPDLVICDEGHRIKN--ITAEISM--ALKAI---RTRRRIVLTGYPLQNNLLEYWCMVD 485
Query: 178 FLDKGKRLGLSFKSFVERW 196
F+ + K LG + K F+ +
Sbjct: 486 FV-RPKYLG-TRKEFINMF 502
>gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 103
Score = 36.4 bits (85), Expect = 0.006
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 3 LVLKPHQIVMVNWLLSHDRCALWASMGSGKTVSVLFALSTIKILDPRPVLIIAP 56
L L+P+QI + LL R + + GSGKT+ L + + VL + P
Sbjct: 2 LELRPYQIEAIRNLLEKKRGLIVMATGSGKTL-TAAKLIARLLKGKKKVLFLVP 54
>gnl|CDD|35571 KOG0350, KOG0350, KOG0350, DEAD-box ATP-dependent RNA helicase [RNA
processing and modification].
Length = 620
Score = 34.2 bits (78), Expect = 0.025
Identities = 44/212 (20%), Positives = 77/212 (36%), Gaps = 47/212 (22%)
Query: 26 ASMGSGKTVSVLFALSTIKILDPRPV-----LIIAPLRVAQYVWKDEVERWSAFSDMTVS 80
A GSGKT++ + + +++L RPV ++I P R D +R ++ + + V
Sbjct: 190 APTGSGKTLA--YVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVC 247
Query: 81 SLIG--SERQRIKALN-------------TPAHL--YIINFENIPWLVKMKLDHWDFATI 123
SL G S + L TP L ++ N ++ L H F +
Sbjct: 248 SLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSF------DLKHLRF--L 299
Query: 124 VVDESTKL--KSFR-------THQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLWG 174
V+DE+ +L +SF+ + T + A + + + L L+
Sbjct: 300 VIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYP 359
Query: 175 QIWFLDKGKRLG------LSFKSFVERWFHTQ 200
+W L L + R FH
Sbjct: 360 PLWKLVFSATLSQDPSKLKDLTLHIPRLFHVS 391
>gnl|CDD|32416 COG2235, ArcA, Arginine deiminase [Amino acid transport and
metabolism].
Length = 409
Score = 31.8 bits (72), Expect = 0.14
Identities = 20/103 (19%), Positives = 43/103 (41%), Gaps = 7/103 (6%)
Query: 84 GSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQT 143
G E +R+ N L F+++P+L K + +H FA I+ ++ ++ +T
Sbjct: 23 GIEIERLTPRNLDDLL----FDDVPYLEKAQKEHDTFAQILREQGIEV--LYLEDLLAET 76
Query: 144 RALGKVAFSKV-KRFIELTGTPSPNGLIDLWGQIWFLDKGKRL 185
A ++ + +++ ++ + LDK K L
Sbjct: 77 LDKANAARNQFIETYLDEAEIKGTGTADEVRAYLLSLDKNKEL 119
>gnl|CDD|36219 KOG1001, KOG1001, KOG1001, Helicase-like transcription factor
HLTF/DNA helicase RAD5, DEAD-box superfamily
[Transcription, Replication, recombination and repair].
Length = 674
Score = 30.0 bits (67), Expect = 0.52
Identities = 40/165 (24%), Positives = 72/165 (43%), Gaps = 25/165 (15%)
Query: 27 SMGSGKTVSVLFALSTIKILDPRPV--------LIIAPLRVAQYVWKDEVERWSAFSDMT 78
MG GKTV + + K+ LI+ P + WK E+E+ + ++
Sbjct: 160 DMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTSLLTQ-WKTELEKVTEEDKLS 218
Query: 79 VSSLIGSERQRIKALNTPAHLYIINFENI--PWLVKMKLDHWDFATIVVDESTKLKSFRT 136
+ G R + K+ + + ++ + LVK+K W IV+DE+ +K
Sbjct: 219 IYVYHG--RTKDKSELNSYDVVLTTYDILKNSPLVKIK---WLR--IVLDEAHTIK---- 267
Query: 137 HQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLWGQIWFLDK 181
++ T+ +A+ ++ K LTGTP N L +L+ FL+
Sbjct: 268 NKDTQIFKAVCQL---DAKYRWCLTGTPIQNNLDELYSLFKFLEI 309
>gnl|CDD|31397 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 29.6 bits (66), Expect = 0.71
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 15 WLLSHDRCALWASMGSGKTV-SVLFALSTIKILDPRPVLIIAPLRVAQYVWKDEVERWSA 73
LLS + + A GSGKT+ ++L LST+ V+ I PL+ +E R
Sbjct: 43 GLLSDENVLISAPTGSGKTLIALLAILSTLLEGG-GKVVYIVPLKALAEEKYEEFSRLEE 101
Query: 74 F 74
Sbjct: 102 L 102
>gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA
processing and modification].
Length = 673
Score = 29.2 bits (65), Expect = 0.87
Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 13/97 (13%)
Query: 4 VLKPHQIV-MVNWLLSHDRCALW-ASMGSGKTVSVLFALSTI-----------KILDPRP 50
+P I L +R + A GSGKT + L L ++
Sbjct: 265 YKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPY 324
Query: 51 VLIIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGSER 87
+I+AP R ++E ++ + S+IG
Sbjct: 325 AIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLS 361
>gnl|CDD|38430 KOG3220, KOG3220, KOG3220, Similar to bacterial dephospho-CoA
kinase [Coenzyme transport and metabolism].
Length = 225
Score = 29.1 bits (65), Expect = 0.91
Identities = 31/137 (22%), Positives = 52/137 (37%), Gaps = 27/137 (19%)
Query: 23 ALWASMGSGK-TVSVLFALSTIKILDPRPVL--IIAP----LRVAQYVWKDEVERWSAFS 75
L + +GK TVS +F I ++D V ++ P R + E+
Sbjct: 5 GLTGGIATGKSTVSQVFKALGIPVIDADVVAREVVEPGTPAYRRIVEAFGTEILLEDGEI 64
Query: 76 DMTV-SSLIGSERQRIKALNTPAHLYI-----------------INFENIPWLVKMKLDH 117
+ V + S+ ++ +ALN H I + +IP L + KL
Sbjct: 65 NRKVLGKRVFSDPKKRQALNKITHPAIRKEMFKEILKLLLRGYRVIVLDIPLLFEAKLLK 124
Query: 118 WDFATIVV--DESTKLK 132
T+VV DE +L+
Sbjct: 125 ICHKTVVVTCDEELQLE 141
>gnl|CDD|31398 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 28.8 bits (64), Expect = 1.1
Identities = 31/129 (24%), Positives = 50/129 (38%), Gaps = 21/129 (16%)
Query: 26 ASMGSGKTVSVLFALSTIKILDP-RPVLIIAPLR-VAQYVWKDEVERWSAF-----SDMT 78
GSGKT S L + + DP L++ P +A D+ ER +T
Sbjct: 92 TGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALAN----DQAERLRELISDLPGKVT 147
Query: 79 VSSLIGSERQ--RIKALNTPAHLYIINFENIPWLVKMKLDHWDFAT-----IVVDESTKL 131
G R + P + + N + + +L+ D W + +VVDE L
Sbjct: 148 FGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDE---L 204
Query: 132 KSFRTHQGT 140
++R QG+
Sbjct: 205 HTYRGVQGS 213
>gnl|CDD|147025 pfam04665, Pox_A32, Poxvirus A32 protein. The A32 protein is
thought to be involved in viral DNA packaging.
Length = 241
Score = 28.1 bits (63), Expect = 1.9
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 21 RCALWASMGSGKTVSVLFALSTIKILDPRPVLIIAPLRVAQY---VWKDEV 68
R A+ GSGKT +L L T+ + + + + P+ Y VW D +
Sbjct: 15 RMAIVGGSGSGKTTYLLSLLRTL-VRKFKHIFLFTPVYNNAYDGYVWPDHI 64
>gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 27.3 bits (60), Expect = 3.1
Identities = 30/149 (20%), Positives = 52/149 (34%), Gaps = 21/149 (14%)
Query: 24 LWASMGSGKTVSVLFALSTIKILDPRP-VLIIAPLRVAQYVWKDEVERWSAFSDMTVSSL 82
+W + GSGKT+++ + L P VL + + DE + + + +
Sbjct: 278 IWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDPKAE 337
Query: 83 IGSE-RQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFAT------IVVDESTKLKSFR 135
SE ++ ++ I I K + +++DE + R
Sbjct: 338 STSELKELLEDGKGK-----IIVTTIQKFNKAVKEDELELLKRKNVVVIIDE-----AHR 387
Query: 136 THQGTKQTRALGKVAFSKVKRFIELTGTP 164
+ G K A K FI TGTP
Sbjct: 388 SQYGELAKLL--KKALKKA-IFIGFTGTP 413
>gnl|CDD|35572 KOG0351, KOG0351, KOG0351, ATP-dependent DNA helicase [Replication,
recombination and repair].
Length = 941
Score = 26.6 bits (58), Expect = 5.8
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 2 HLVLKPHQIVMVNWLLSHDRCALWASMGSGKTVSVLFALSTIKILDPRPVLIIAPLR 58
H +P+Q+ +N LS C + G GK S+ + L +L ++I+PL
Sbjct: 262 HKGFRPNQLEAINATLSGKDCFVLMPTGGGK--SLCYQLPA--LLLGGVTVVISPLI 314
>gnl|CDD|36180 KOG0962, KOG0962, KOG0962, DNA repair protein RAD50, ABC-type
ATPase/SMC superfamily [Replication, recombination and
repair].
Length = 1294
Score = 26.4 bits (58), Expect = 6.3
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 139 GTKQTRALGKVAFSKVK-------RFIELTGTPSPNGLIDLWGQIWFLDKGKRLGLSFKS 191
G + RA K+AF+ V R I+LT + L IW ++ G R+ LS +S
Sbjct: 72 GETEVRAQVKLAFTDVNGETMICTRTIQLTQKRTKMEFKTLESVIWAINDGDRVTLSGRS 131
>gnl|CDD|31393 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 26.3 bits (58), Expect = 6.9
Identities = 31/147 (21%), Positives = 57/147 (38%), Gaps = 19/147 (12%)
Query: 29 GSGKTVSVLFALSTIKILDPRPVLIIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGSER- 87
GSGKTV L A+ I ++AP + + + +W + V+ L GS +
Sbjct: 293 GSGKTVVALLAMLAA-IEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKG 351
Query: 88 -QRIKAL----NTPAHLYIINFENIPWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQ 142
R + L + + + L++ K++ + +++DE + G Q
Sbjct: 352 KARKEILEQLASGEIDIVV----GTHALIQDKVEFHNLGLVIIDEQHRF-------GVHQ 400
Query: 143 TRALGKVAFSKVKRFIELTGTPSPNGL 169
AL + + +T TP P L
Sbjct: 401 RLALREKGEQNP-HVLVMTATPIPRTL 426
>gnl|CDD|33754 COG3973, COG3973, Superfamily I DNA and RNA helicases [General
function prediction only].
Length = 747
Score = 26.1 bits (57), Expect = 7.2
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 29 GSGKTVSVLFALSTI-----KILDPRPVLIIAPLRV-AQYV 63
GSGKT L ++ + L +PVL++ P RV +Y+
Sbjct: 236 GSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYI 276
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
0.323 0.136 0.426
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,749,093
Number of extensions: 137789
Number of successful extensions: 350
Number of sequences better than 10.0: 1
Number of HSP's gapped: 340
Number of HSP's successfully gapped: 38
Length of query: 220
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 130
Effective length of database: 4,318,927
Effective search space: 561460510
Effective search space used: 561460510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.9 bits)