BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 002357
(931 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 787 bits (2032), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 430/972 (44%), Positives = 603/972 (62%), Gaps = 87/972 (8%)
Query: 34 LTRSCVHEVAVPSGYALTKDEAIHGTFANPVYNGEM---AKTYSFELDPFQRVSVACLER 90
L+ H+VA+P Y T P+ + A+TY F LDPFQ +++C++R
Sbjct: 150 LSHQVRHQVALPPNYDYT-----------PIAEHKRVNEARTYPFTLDPFQDTAISCIDR 198
Query: 91 NESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKALSNQKYRELHQEFKDVGLMT 150
ESVLVSAHTSAGKT VAEYAIA + ++KQRVIYTSP+KALSNQKYREL EF DVGLMT
Sbjct: 199 GESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMT 258
Query: 151 GDVTLSPNASCLVMTTEILRGMLYRGSEVLKEVAWVIFDEIHYMKDRERGVVWEESIIFL 210
GD+T++P+A CLVMTTEILR MLYRGSEV++EVAWVIFDE+HYM+D+ERGVVWEE+II L
Sbjct: 259 GDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILL 318
Query: 211 PPAIKMVFLSATMSNATQFAEWICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVD 270
P ++ VFLSAT+ NA +FAEWIC +H QPCH+VYT+FRPTPLQHY+FP G G+YLVVD
Sbjct: 319 PDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVD 378
Query: 271 EKEQFREDNFVKLQDTFLKQKIGGRRENXXX-----XXXXXXXXXXXXXXDIFKIVKMIM 325
EK FRE+NF K + Q IG + DI+KIVKMI
Sbjct: 379 EKSTFREENFQKAMASISNQ-IGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIW 437
Query: 326 ERKFQPVIVFSFSRRECEQHAMSMSKLDFNTQEEKDTVEQVFQNAVDCLNEEDRNLPAIE 385
++K+ PVIVFSFS+R+CE+ A+ MSKLDFN+ +EK+ + ++F NA+ L E DR LP I+
Sbjct: 438 KKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIK 497
Query: 386 LMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLVKALFATETFAMGLNMPAKTVVFTAVK 445
+LPLL+RGI +HHSGLLP++KE++E+LFQEG +K LFATETF++GLNMPAKTVVFT+V+
Sbjct: 498 HILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVR 557
Query: 446 KWDGDSHRYIGSGEYIQMSXXXXXXXXXXXXICIIMVDEQMEMNTLKDMV------LEGQ 499
KWDG R++ GEYIQMS I I+M+DE+ME K MV L+
Sbjct: 558 KWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSA 617
Query: 500 F----------------TAEHVIKNSFHQFQYEKALPDIGKKVSKLEEEAASLDASGEAE 543
F + E ++++SF QFQ ++P + KK+++L+++ ++ E
Sbjct: 618 FHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEEN 677
Query: 544 VAEYHKLKLDIAQLEKKLMSEITRPERVLYYLGSGRL--IKVREXXXXXXXXXXXXXXXX 601
V EYH+++ I + + +T P L +L GRL I V
Sbjct: 678 VKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRI 737
Query: 602 XXXXXGTLPSRGGGYIVPVQLPLISTLSKIRL------SVPPDLRPLDARQSILLAV--- 652
+ + YIV V + + S + L ++P +RP + + + AV
Sbjct: 738 NKRNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPI 797
Query: 653 --------------------------------QELESRFPQGLPKLNPVKDMKIEDPEVV 680
+E+ RFP G+P L+PVK+MKIED + +
Sbjct: 798 TLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFL 857
Query: 681 DLVNQIEELEHKLFAHPLNKSQDENQIRC-FQRKAEVNHEIQQLKSKMRDSQIQKFRDEL 739
L+ +I+ L KL ++PL S ++ + RK +++ +++QLK K+ +SQ D+L
Sbjct: 858 KLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDL 917
Query: 740 KNRSRVLKKLGHIDADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASC 799
+ R RVL++LG + +++LKGR AC I +GDELL+TEL+FNG FN+L Q AAL SC
Sbjct: 918 RRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC 977
Query: 800 FIPVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVI 859
F ++ E L+ ELA+PL+ ++E A KIA+I + K+EV +YVES R LM+V+
Sbjct: 978 FAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVES-FRHELMEVV 1036
Query: 860 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESL 919
Y W +GATF ++ +MTD++EGS+IR +RL+E + +L A +G +L++K A + +
Sbjct: 1037 YEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLI 1096
Query: 920 RRGIMFSNSLYL 931
R I+ + SLYL
Sbjct: 1097 HRDIVSAGSLYL 1108
>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
Length = 1010
Score = 786 bits (2031), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 430/972 (44%), Positives = 602/972 (61%), Gaps = 87/972 (8%)
Query: 34 LTRSCVHEVAVPSGYALTKDEAIHGTFANPVYNGEM---AKTYSFELDPFQRVSVACLER 90
L+ H+VA+P Y T P+ + A+TY F LDPFQ +++C++R
Sbjct: 52 LSHQVRHQVALPPNYDYT-----------PIAEHKRVNEARTYPFTLDPFQDTAISCIDR 100
Query: 91 NESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKALSNQKYRELHQEFKDVGLMT 150
ESVLVSAHTSAGKT VAEYAIA + ++KQRVIYTSP+KALSNQKYREL EF DVGLMT
Sbjct: 101 GESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMT 160
Query: 151 GDVTLSPNASCLVMTTEILRGMLYRGSEVLKEVAWVIFDEIHYMKDRERGVVWEESIIFL 210
GD+T++P+A CLVMTTEILR MLYRGSEV++EVAWVIFDE+HYM+D+ERGVVWEE+II L
Sbjct: 161 GDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILL 220
Query: 211 PPAIKMVFLSATMSNATQFAEWICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVD 270
P ++ VFLSAT+ NA +FAEWIC +H QPCH+VYT+FRPTPLQHY+FP G G+YLVVD
Sbjct: 221 PDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVD 280
Query: 271 EKEQFREDNFVKLQDTFLKQKIGG-----RRENXXXXXXXXXXXXXXXXXDIFKIVKMIM 325
EK FRE+NF K + Q IG DI+KIVKMI
Sbjct: 281 EKSTFREENFQKAMASISNQ-IGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIW 339
Query: 326 ERKFQPVIVFSFSRRECEQHAMSMSKLDFNTQEEKDTVEQVFQNAVDCLNEEDRNLPAIE 385
++K+ PVIVFSFS+R+CE+ A+ MSKLDFN+ +EK+ + ++F NA+ L E DR LP I+
Sbjct: 340 KKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIK 399
Query: 386 LMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLVKALFATETFAMGLNMPAKTVVFTAVK 445
+LPLL+RGI +HHSGLLP++KE++E+LFQEG +K LFATETF++GLNMPAKTVVFT+V+
Sbjct: 400 HILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVR 459
Query: 446 KWDGDSHRYIGSGEYIQMSXXXXXXXXXXXXICIIMVDEQMEMNTLKDMV------LEGQ 499
KWDG R++ GEYIQMS I I+M+DE+ME K MV L+
Sbjct: 460 KWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSA 519
Query: 500 F----------------TAEHVIKNSFHQFQYEKALPDIGKKVSKLEEEAASLDASGEAE 543
F + E ++++SF QFQ ++P + KK+++L+++ ++ E
Sbjct: 520 FHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEEN 579
Query: 544 VAEYHKLKLDIAQLEKKLMSEITRPERVLYYLGSGRL--IKVREXXXXXXXXXXXXXXXX 601
V EYH+++ I + + +T P L +L GRL I V
Sbjct: 580 VKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRI 639
Query: 602 XXXXXGTLPSRGGGYIVPVQLPLISTLSKIRL------SVPPDLRPLDARQSILLAV--- 652
+ + YIV V + + S + L ++P +RP + + + AV
Sbjct: 640 NKRNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPI 699
Query: 653 --------------------------------QELESRFPQGLPKLNPVKDMKIEDPEVV 680
+E+ RFP G+P L+PVK+MKIED + +
Sbjct: 700 TLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFL 759
Query: 681 DLVNQIEELEHKLFAHPLNKSQDENQIRC-FQRKAEVNHEIQQLKSKMRDSQIQKFRDEL 739
L+ +I+ L KL ++PL S ++ + RK +++ +++QLK K+ +SQ D+L
Sbjct: 760 KLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDL 819
Query: 740 KNRSRVLKKLGHIDADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASC 799
+ R RVL++LG + +++LKGR AC I +GDELL+TEL+FNG FN+L Q AAL SC
Sbjct: 820 RRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC 879
Query: 800 FIPVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVI 859
F ++ E L+ ELA+PL+ ++E A KIA+I + K+EV +YVES R LM+V+
Sbjct: 880 FAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVES-FRHELMEVV 938
Query: 860 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESL 919
Y W +GATF ++ +MTD++EGS+IR +RL+E + +L A +G +L++K A + +
Sbjct: 939 YEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLI 998
Query: 920 RRGIMFSNSLYL 931
R I+ + SLYL
Sbjct: 999 HRDIVSAGSLYL 1010
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 235 bits (600), Expect = 7e-62, Method: Compositional matrix adjust.
Identities = 112/215 (52%), Positives = 158/215 (73%), Gaps = 4/215 (1%)
Query: 70 AKTYSFELDPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLK 129
A+++ FELD FQ+ +V LE+ +SV V+AHTSAGKT VAEYAIAMA R+ + IYTSP+K
Sbjct: 33 ARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIK 92
Query: 130 ALSNQKYRELHQEFKDV--GLMTGDVTLSPNASCLVMTTEILRGMLYRGSEVLKEVAWVI 187
ALSNQK+R+ + F DV GL+TGDV ++P+A+CL+MTTEILR MLYRG++++++V +VI
Sbjct: 93 ALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVI 152
Query: 188 FDEIHYMKDRERGVVWEESIIFLPPAIKMVFLSATMSNATQFAEWICHLHKQPCHVVYTD 247
FDE+HY+ D++RGVVWEE II LP +K + LSAT+ N +FA WI ++ +V+ T
Sbjct: 153 FDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTYEFANWIGRTKQKNIYVISTP 212
Query: 248 FRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVK 282
RP PL+ ++ L V+++ +F E NF K
Sbjct: 213 KRPVPLEINIW--AKKELIPVINQNSEFLEANFRK 245
Score = 169 bits (427), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 95/294 (32%), Positives = 162/294 (55%), Gaps = 27/294 (9%)
Query: 319 KIVKMIMERKFQPVIVFSFSRRECEQHAMSMSKLDFNTQEEKDTVEQVFQNAVDCLNEED 378
+IV + +R+ P++VF FS++ CE++A + ++F +EK + + ++ L +ED
Sbjct: 326 EIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKED 385
Query: 379 RNLPAIELMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLVKALFATETFAMGLNMPAKT 438
R+LP I LL+RGIAVHH GLLP++KEL+E+LF +G +K LFATETFAMGLN+P +T
Sbjct: 386 RDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRT 445
Query: 439 VVFTAVKKWDGDSHRYIGSGEYIQMSXXXXXXXXXXXXICIIMV-DEQMEMNTLKDMV-- 495
V+F++++K DG+ R + GE+ QM+ I+M + + + T K++
Sbjct: 446 VIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEVTMG 505
Query: 496 ----LEGQF----------------TAEHVIKNSFHQFQYEKALPDIGKKVSKLEEEAAS 535
L+ QF E +IK SF + E P+ K++ L+EE +
Sbjct: 506 VPTRLQSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAKETLQPEHEKQIKVLQEELQT 565
Query: 536 LDASG----EAEVAEYHKLKLDIAQLEKKLMSEITRPERVLYYLGSGRLIKVRE 585
++ + ++ ++ +L L + LM E+ + +L+ L GRL+ R+
Sbjct: 566 IEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRD 619
Score = 105 bits (263), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 70/221 (31%), Positives = 122/221 (55%), Gaps = 8/221 (3%)
Query: 716 VNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGHIDADGVVQLKGRAACLIDTGDELL 775
+ +I++L M D + D K R VLK ID + V LKGR AC I++G EL+
Sbjct: 780 IKKKIEELYHLMSDQNLSLLPDYEK-RLAVLKDTEFIDQNHNVLLKGRVACEINSGYELV 838
Query: 776 VTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQ----INLRMELAKPLQQLQESARKIA 831
+TEL+ + + ++ AL S F+ K+ E+ + R LAK Q+++E +K+
Sbjct: 839 LTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEPPIVTPR--LAKGKQRIEEIYKKML 896
Query: 832 EIQNECKLEVNVDEYVESTVRPF-LMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLD 890
+ N ++ + DE + F +M+V+Y W++G +F E+++M+ EG+++R LD
Sbjct: 897 CVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLD 956
Query: 891 EFLNQLRAAAQAVGEVNLEKKFAAASESLRRGIMFSNSLYL 931
E +++ A+ +G L K + A E ++R I+F+ SLYL
Sbjct: 957 EICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL 997
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 126 bits (317), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 115/408 (28%), Positives = 195/408 (47%), Gaps = 69/408 (16%)
Query: 76 ELDPFQRVSV--ACLERNESVLVSAHTSAGKTAVAEYAI-AMAFRDKQRVIYTSPLKALS 132
+L+P Q +V LE N +L+++ T +GKT +AE I + ++ + IY +PL+AL+
Sbjct: 30 KLNPPQTEAVKKGLLEGNR-LLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALT 88
Query: 133 NQKYRELHQEFKD-------VGLMTGDVTLS----PNASCLVMTTEILRGMLYRGSEVLK 181
N+KY FKD V + +GD N ++ T E L + E L
Sbjct: 89 NEKY----LTFKDWELIGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLN 144
Query: 182 EVAWVIFDEIHYMKDRERGVVWEESIIFLPPAIKMVFLSATMSNATQFAEWICHLHKQPC 241
EV + + DE+HY+ D ERG V ES+ ++ LSAT+SN Q A+W L +P
Sbjct: 145 EVNYFVLDELHYLNDPERGPV-VESVTIRAKRRNLLALSATISNYKQIAKW---LGAEP- 199
Query: 242 HVVYTDFRPTPL-QHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTFLKQKIGGRRENXX 300
V T++RP PL + ++P E+ +++ V +D K+ G
Sbjct: 200 --VATNWRPVPLIEGVIYP-------------ERKKKEYNVIFKDNTTKKVHG------- 237
Query: 301 XXXXXXXXXXXXXXXDIFKIVKMIMERKFQPVIVFSFSRRECEQHAMSMSK-LDFNTQEE 359
D + K V+VF SR+ E A+ ++ ++F + +E
Sbjct: 238 --------------DDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDE 283
Query: 360 KDTVEQVFQNAVDCLNEEDRNLPAIELMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLV 419
+ + ++ + D E+ EL+ L+ +G+A HH+GL +++L+E F++ +
Sbjct: 284 -NALSEILKQLDDI---EEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKI 339
Query: 420 KALFATETFAMGLNMPAKTVVFTAVKKWDGDSHRY---IGSGEYIQMS 464
K + AT T A G+N+PA+TV+ + +++ Y I EY QMS
Sbjct: 340 KVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMS 387
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 110 bits (274), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 103/399 (25%), Positives = 177/399 (44%), Gaps = 66/399 (16%)
Query: 76 ELDPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKALSNQK 135
EL P Q +V + +++L++ T+AGKT +AE A+ + +Y PL+AL+ +K
Sbjct: 25 ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEK 84
Query: 136 YRELHQEFK---DVGLMTGDVTLS----PNASCLVMTTEILRGMLYRGSEVLKEVAWVIF 188
Y + K +G+ TGD + +V T+E ++ + +K V+ ++
Sbjct: 85 YESFKKWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVV 144
Query: 189 DEIHYMKDRERGVVWE---ESIIFLPPAIKMVFLSATMSNATQFAEWICHLHKQPCHVVY 245
DEIH + +RG E + + A++++ LSAT N T+ AEW+
Sbjct: 145 DEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNVTEIAEWL------DADYYV 198
Query: 246 TDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTFLKQKIGGRRENXXXXXXX 305
+D+RP PL V G L L R F +L + + + G
Sbjct: 199 SDWRPVPLVEGVLCEG--TLELFDGAFSTSRRVKFEELVEECVAENGG------------ 244
Query: 306 XXXXXXXXXXDIFKIVKMIMERKFQPVIVFSFSRRECEQHAMSMSKLDFNTQEEKDTVEQ 365
V+VF +RR E+ A+ +S + E + +
Sbjct: 245 --------------------------VLVFESTRRGAEKTAVKLSAITAKYVENEGLEKA 278
Query: 366 VFQNAVDCLNEEDRNLPAIELMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLVKALFAT 425
+ + NE + + E +++G A HH+GLL + +VE F+ G +K + AT
Sbjct: 279 ILEE-----NEGEMSRKLAE----CVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVAT 329
Query: 426 ETFAMGLNMPAKTVVFTAVKKWDGDSHRYIGSGEYIQMS 464
T A G+N+PA+ V+ ++ ++DG S R I EY QM+
Sbjct: 330 PTLAAGVNLPARRVIVRSLYRFDGYSKR-IKVSEYKQMA 367
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 105 bits (262), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 94/368 (25%), Positives = 168/368 (45%), Gaps = 68/368 (18%)
Query: 91 NESVLVSAHTSAGKTAVAEYAIAMAFR---DKQRVIYTSPLKALSNQKYRELHQEFKDVG 147
++ L+S T++GKT +AE IAM R + +Y PLKAL+ +K++E Q+++ +G
Sbjct: 39 GKNALISIPTASGKTLIAE--IAMVHRILTQGGKAVYIVPLKALAEEKFQEF-QDWEKIG 95
Query: 148 L----MTGDVTLSP----NASCLVMTTEILRGMLYRGSEVLKEVAWVIFDEIHYMKDRER 199
L TGD ++ T E +L GS +K+V ++ DEIH + R+R
Sbjct: 96 LRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDR 155
Query: 200 GVVWEESIIFLPPAIKMVFLSATMSNATQFAEWICHLHKQPCHVVYTDFRPTPLQHYVFP 259
G E + + +++ LSAT+ N + AEW+ ++ +D+RP L+ VF
Sbjct: 156 GATLEVILAHMLGKAQIIGLSATIGNPEELAEWLN------AELIVSDWRPVKLRRGVFY 209
Query: 260 VGGSGLYLVVDEKEQFREDNFVKLQDTFLKQKIGGRRENXXXXXXXXXXXXXXXXXDIFK 319
G FV +D + + ++
Sbjct: 210 QG------------------FVTWEDGSIDR-------------------FSSWEELVYD 232
Query: 320 IVKMIMERKFQPVIVFSFSRRECEQHAMSMSKLDFNTQEEKDTVEQVFQNAVDCLNEEDR 379
+ RK + ++F RR+ E+ A+ +SK + K + + A++ L +
Sbjct: 233 AI-----RKKKGALIFVNMRRKAERVALELSK------KVKSLLTKPEIRALNELADSLE 281
Query: 380 NLPAIELMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLVKALFATETFAMGLNMPAKTV 439
P E + ++ G+A HH+GL + LVE F++G++KA+ AT T + G+N PA V
Sbjct: 282 ENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRV 341
Query: 440 VFTAVKKW 447
+ + ++
Sbjct: 342 IIRDIWRY 349
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 82.4 bits (202), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 101/417 (24%), Positives = 174/417 (41%), Gaps = 94/417 (22%)
Query: 86 ACLERNESVLVSAHTSAGKTAVAEYAIAMAFR-----------DKQRVIYTSPLKALSNQ 134
A LE +E++L+ A T AGKT VA + D ++IY +P+++L +
Sbjct: 90 AALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQE 149
Query: 135 KYRELHQEFKDVGL----MTGDVTLSPN----ASCLVMTTEILRGMLYRGSE--VLKEVA 184
+ G+ +TGD L +V T E + +G E + V
Sbjct: 150 MVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVR 209
Query: 185 WVIFDEIHYMKDRERGVVWE-------ESIIFLPPAIKMVFLSATMSNATQFAEWICHLH 237
+I DEIH + D +RG V E +I ++++ LSAT+ N A + L
Sbjct: 210 LIILDEIHLLHD-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATF---LR 265
Query: 238 KQPCHVVY---TDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTFLKQKI-- 292
P ++ FRP PL+ Y+ + EK+ + ++ + + +KI
Sbjct: 266 VDPAKGLFYFDNSFRPVPLEQ---------TYVGITEKKAIKR---FQIMNEIVYEKIME 313
Query: 293 -GGRRENXXXXXXXXXXXXXXXXXDIFKIVKMIMERKFQPVIVFSFSRRECEQHAMSMSK 351
G+ + V+VF SR+E + A ++
Sbjct: 314 HAGKNQ----------------------------------VLVFVHSRKETGKTARAIRD 339
Query: 352 LDFNTQEEKDTVEQVFQN---AVDCLNEEDRNLPAIELMLPLLKRGIAVHHSGLLPVIKE 408
+ EKDT+ + + + L E +EL LL G A+HH+G+ V +
Sbjct: 340 MCL----EKDTLGLFLREGSASTEVLRTEAEQCKNLELK-DLLPYGFAIHHAGMTRVDRT 394
Query: 409 LVELLFQEGLVKALFATETFAMGLNMPAKTVVFTAVKKWDGDSHRY--IGSGEYIQM 463
LVE LF + ++ L +T T A G+N+PA TV+ + + + R+ +G+ + +QM
Sbjct: 395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQM 451
Score = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 57/209 (27%), Positives = 101/209 (48%), Gaps = 37/209 (17%)
Query: 77 LDPFQ-RVSVACLERNESVLVSAHTSAGKTAVAEYAIA-MAFRDKQ-RVIYTSPLKALSN 133
+P Q +V +++V V A T +GKT AE+AI M + + R +Y +P++AL+
Sbjct: 927 FNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAE 986
Query: 134 QKYRELHQEFKD-----VGLMTG----DVTLSPNASCLVMTTEI--LRGMLYRGSEVLKE 182
Q Y + +++F+D V L+TG D+ L + ++ T E + ++ + ++
Sbjct: 987 QVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQN 1046
Query: 183 VAWVIFDEIHYMKDRERGVVWE---------ESIIFLPPAIKMVFLSATMSNATQFAEWI 233
+ + DE+H + E G V E S I P I++V LS+++SNA A W+
Sbjct: 1047 INLFVVDEVHLIGG-ENGPVLEVICSRMRYISSQIERP--IRIVALSSSLSNAKDVAHWL 1103
Query: 234 CHLHKQPCHVVYT-----DFRPTPLQHYV 257
C T + RP PL+ ++
Sbjct: 1104 G------CSATSTFNFHPNVRPVPLELHI 1126
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 50/198 (25%), Positives = 82/198 (41%), Gaps = 29/198 (14%)
Query: 330 QPVIVFSFSRRECEQHAMSMSKLDFNTQEEKDTVEQVFQNAVDCLNEEDRNLPAIE---- 385
+PVIVF SR++ ++ +D T D Q F + C E+D +P +E
Sbjct: 1156 KPVIVFVPSRKQTR-----LTAIDILTTCAADIQRQRF---LHC-TEKDL-IPYLEKLSD 1205
Query: 386 -LMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLVKALFATETFAMGLNMPAKTVVFTAV 444
+ L G+ H GL P+ + LVE LF G ++ + A+ + G+N+ A V+
Sbjct: 1206 STLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDT 1265
Query: 445 KKWDGDSHRYIGSGEY--IQMSXXXXXXXXXXXXICIIMVD------------EQMEMNT 490
+ ++G H Y+ Y +QM C+IM E + + +
Sbjct: 1266 QYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVES 1325
Query: 491 LKDMVLEGQFTAEHVIKN 508
D + F AE V K
Sbjct: 1326 HLDHCMHDHFNAEIVTKT 1343
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 82.4 bits (202), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 101/417 (24%), Positives = 174/417 (41%), Gaps = 94/417 (22%)
Query: 86 ACLERNESVLVSAHTSAGKTAVAEYAIAMAFR-----------DKQRVIYTSPLKALSNQ 134
A LE +E++L+ A T AGKT VA + D ++IY +P+++L +
Sbjct: 90 AALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQE 149
Query: 135 KYRELHQEFKDVGL----MTGDVTLSPN----ASCLVMTTEILRGMLYRGSE--VLKEVA 184
+ G+ +TGD L +V T E + +G E + V
Sbjct: 150 MVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVR 209
Query: 185 WVIFDEIHYMKDRERGVVWE-------ESIIFLPPAIKMVFLSATMSNATQFAEWICHLH 237
+I DEIH + D +RG V E +I ++++ LSAT+ N A + L
Sbjct: 210 LIILDEIHLLHD-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATF---LR 265
Query: 238 KQPCHVVY---TDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTFLKQKI-- 292
P ++ FRP PL+ Y+ + EK+ + ++ + + +KI
Sbjct: 266 VDPAKGLFYFDNSFRPVPLEQ---------TYVGITEKKAIKR---FQIMNEIVYEKIME 313
Query: 293 -GGRRENXXXXXXXXXXXXXXXXXDIFKIVKMIMERKFQPVIVFSFSRRECEQHAMSMSK 351
G+ + V+VF SR+E + A ++
Sbjct: 314 HAGKNQ----------------------------------VLVFVHSRKETGKTARAIRD 339
Query: 352 LDFNTQEEKDTVEQVFQN---AVDCLNEEDRNLPAIELMLPLLKRGIAVHHSGLLPVIKE 408
+ EKDT+ + + + L E +EL LL G A+HH+G+ V +
Sbjct: 340 MCL----EKDTLGLFLREGSASTEVLRTEAEQCKNLELK-DLLPYGFAIHHAGMTRVDRT 394
Query: 409 LVELLFQEGLVKALFATETFAMGLNMPAKTVVFTAVKKWDGDSHRY--IGSGEYIQM 463
LVE LF + ++ L +T T A G+N+PA TV+ + + + R+ +G+ + +QM
Sbjct: 395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQM 451
Score = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 57/209 (27%), Positives = 101/209 (48%), Gaps = 37/209 (17%)
Query: 77 LDPFQ-RVSVACLERNESVLVSAHTSAGKTAVAEYAIA-MAFRDKQ-RVIYTSPLKALSN 133
+P Q +V +++V V A T +GKT AE+AI M + + R +Y +P++AL+
Sbjct: 927 FNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAE 986
Query: 134 QKYRELHQEFKD-----VGLMTG----DVTLSPNASCLVMTTEI--LRGMLYRGSEVLKE 182
Q Y + +++F+D V L+TG D+ L + ++ T E + ++ + ++
Sbjct: 987 QVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQN 1046
Query: 183 VAWVIFDEIHYMKDRERGVVWE---------ESIIFLPPAIKMVFLSATMSNATQFAEWI 233
+ + DE+H + E G V E S I P I++V LS+++SNA A W+
Sbjct: 1047 INLFVVDEVHLIGG-ENGPVLEVICSRMRYISSQIERP--IRIVALSSSLSNAKDVAHWL 1103
Query: 234 CHLHKQPCHVVYT-----DFRPTPLQHYV 257
C T + RP PL+ ++
Sbjct: 1104 G------CSATSTFNFHPNVRPVPLELHI 1126
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 50/198 (25%), Positives = 82/198 (41%), Gaps = 29/198 (14%)
Query: 330 QPVIVFSFSRRECEQHAMSMSKLDFNTQEEKDTVEQVFQNAVDCLNEEDRNLPAIE---- 385
+PVIVF SR++ ++ +D T D Q F + C E+D +P +E
Sbjct: 1156 KPVIVFVPSRKQTR-----LTAIDILTTCAADIQRQRF---LHC-TEKDL-IPYLEKLSD 1205
Query: 386 -LMLPLLKRGIAVHHSGLLPVIKELVELLFQEGLVKALFATETFAMGLNMPAKTVVFTAV 444
+ L G+ H GL P+ + LVE LF G ++ + A+ + G+N+ A V+
Sbjct: 1206 STLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDT 1265
Query: 445 KKWDGDSHRYIGSGEY--IQMSXXXXXXXXXXXXICIIMVD------------EQMEMNT 490
+ ++G H Y+ Y +QM C+IM E + + +
Sbjct: 1266 QYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVES 1325
Query: 491 LKDMVLEGQFTAEHVIKN 508
D + F AE V K
Sbjct: 1326 HLDHCMHDHFNAEIVTKT 1343
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 34.3 bits (77), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 66/175 (37%), Gaps = 17/175 (9%)
Query: 79 PFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFR---DKQRVIYTSPLKALSNQK 135
P Q ++ +L A GKTA + +K + + P + L+ Q
Sbjct: 46 PIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQT 105
Query: 136 YRELHQEFKDVGL----MTGDVTLSPNASCLVMTTEILRG-------MLYRGSEVLKEVA 184
+ + K G+ TG L + L T IL G + R L + +
Sbjct: 106 SQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCS 165
Query: 185 WVIFDEIHYMKDRERGVVWEESIIFLPPAIKMVFLSATMS-NATQFAEWICHLHK 238
I DE M R+ + E+ + FLPP + + SAT +F + HLHK
Sbjct: 166 LFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEF--MVKHLHK 218
>pdb|2DFS|A Chain A, 3-D Structure Of Myosin-V Inhibited State
pdb|2DFS|M Chain M, 3-D Structure Of Myosin-V Inhibited State
Length = 1080
Score = 33.5 bits (75), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 11/61 (18%)
Query: 63 PVYNGEMAKTYSFE----LDPF-------QRVSVACLERNESVLVSAHTSAGKTAVAEYA 111
P+Y ++ YS + +DP +A ERN+S++VS + AGKT A+YA
Sbjct: 117 PIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYA 176
Query: 112 I 112
+
Sbjct: 177 M 177
>pdb|1OE9|A Chain A, Crystal Structure Of Myosin V Motor With Essential Light
Chain - Nucleotide-Free
pdb|1W7I|A Chain A, Crystal Structure Of Myosin V Motor Without Nucleotide
Soaked In 10 Mm Mgadp
pdb|1W7J|A Chain A, Crystal Structure Of Myosin V Motor With Essential Light
Chain + Adp-Befx - Near Rigor
Length = 795
Score = 33.1 bits (74), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 11/61 (18%)
Query: 63 PVYNGEMAKTYSFE----LDPF-------QRVSVACLERNESVLVSAHTSAGKTAVAEYA 111
P+Y ++ YS + +DP +A ERN+S++VS + AGKT A+YA
Sbjct: 117 PIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYA 176
Query: 112 I 112
+
Sbjct: 177 M 177
>pdb|1W8J|A Chain A, Crystal Structure Of Myosin V Motor Domain -
Nucleotide-Free
pdb|1W8J|B Chain B, Crystal Structure Of Myosin V Motor Domain -
Nucleotide-Free
pdb|1W8J|C Chain C, Crystal Structure Of Myosin V Motor Domain -
Nucleotide-Free
pdb|1W8J|D Chain D, Crystal Structure Of Myosin V Motor Domain -
Nucleotide-Free
Length = 766
Score = 32.7 bits (73), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 11/61 (18%)
Query: 63 PVYNGEMAKTYSF----ELDPF-------QRVSVACLERNESVLVSAHTSAGKTAVAEYA 111
P+Y ++ YS ++DP +A ERN+S++VS + AGKT A+YA
Sbjct: 117 PIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYA 176
Query: 112 I 112
+
Sbjct: 177 M 177
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 50/236 (21%), Positives = 90/236 (38%), Gaps = 37/236 (15%)
Query: 73 YSFEL-DPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKAL 131
Y FE Q+ ++ + + V+ + + GKTA ++ I +AL
Sbjct: 19 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLD-----IQVRETQAL 73
Query: 132 SNQKYRELHQEFKDVGLMTGDVTLSPNASCLVMTT--EILRGMLYRGSEVLKEVAWVIFD 189
REL + + L GD + +C+ T E +R + Y G V+ +FD
Sbjct: 74 ILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFD 132
Query: 190 EIHYMKDRERGVV--------------WEESII----FLPPAIKMVFLSATMSNATQFAE 231
I R R + ++E I +LPPA ++V +SAT+ + + E
Sbjct: 133 MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH--EVLE 190
Query: 232 WICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTF 287
P ++ ++ + G + V E+E+++ D L DT
Sbjct: 191 MTNKFMTDPIRIL--------VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 238
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 79 PFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQ----RVIYTSPLKALSNQ 134
P Q ++ + +L SA T +GKT I M + R + SP + L++Q
Sbjct: 54 PIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQ 113
Query: 135 KYREL 139
+REL
Sbjct: 114 IHREL 118
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 50/236 (21%), Positives = 89/236 (37%), Gaps = 37/236 (15%)
Query: 73 YSFEL-DPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKAL 131
Y FE Q+ ++ + + V+ + + GKTA ++ I +AL
Sbjct: 56 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLD-----IQVRETQAL 110
Query: 132 SNQKYRELHQEFKDVGLMTGDVTLSPNASCLVMTT--EILRGMLYRGSEVLKEVAWVIFD 189
REL + + L GD +C+ T E +R + Y G V+ +FD
Sbjct: 111 ILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFD 169
Query: 190 EIHYMKDRERGVV--------------WEESII----FLPPAIKMVFLSATMSNATQFAE 231
I R R + ++E I +LPPA ++V +SAT+ + + E
Sbjct: 170 MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH--EILE 227
Query: 232 WICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTF 287
P ++ ++ + G + V E+E+++ D L DT
Sbjct: 228 MTNKFMTDPIRIL--------VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 275
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 50/236 (21%), Positives = 89/236 (37%), Gaps = 37/236 (15%)
Query: 73 YSFEL-DPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKAL 131
Y FE Q+ ++ + + V+ + + GKTA ++ I +AL
Sbjct: 55 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLD-----IQVRETQAL 109
Query: 132 SNQKYRELHQEFKDVGLMTGDVTLSPNASCLVMTT--EILRGMLYRGSEVLKEVAWVIFD 189
REL + + L GD +C+ T E +R + Y G V+ +FD
Sbjct: 110 ILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFD 168
Query: 190 EIHYMKDRERGVV--------------WEESII----FLPPAIKMVFLSATMSNATQFAE 231
I R R + ++E I +LPPA ++V +SAT+ + + E
Sbjct: 169 MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH--EILE 226
Query: 232 WICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTF 287
P ++ ++ + G + V E+E+++ D L DT
Sbjct: 227 MTNKFMTDPIRIL--------VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 274
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 50/236 (21%), Positives = 89/236 (37%), Gaps = 37/236 (15%)
Query: 73 YSFEL-DPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKAL 131
Y FE Q+ ++ + + V+ + + GKTA ++ I +AL
Sbjct: 56 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLD-----IQVRETQAL 110
Query: 132 SNQKYRELHQEFKDVGLMTGDVTLSPNASCLVMTT--EILRGMLYRGSEVLKEVAWVIFD 189
REL + + L GD +C+ T E +R + Y G V+ +FD
Sbjct: 111 ILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFD 169
Query: 190 EIHYMKDRERGVV--------------WEESII----FLPPAIKMVFLSATMSNATQFAE 231
I R R + ++E I +LPPA ++V +SAT+ + + E
Sbjct: 170 MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH--EILE 227
Query: 232 WICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTF 287
P ++ ++ + G + V E+E+++ D L DT
Sbjct: 228 MTNKFMTDPIRIL--------VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 275
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 27/137 (19%), Positives = 53/137 (38%), Gaps = 19/137 (13%)
Query: 79 PFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRD--------KQRVIYTSPLKA 130
P Q+ S+ + ++ A T +GKTA I + + +V+ SP +
Sbjct: 81 PIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRE 140
Query: 131 LSNQKYRELH----QEFKDVGLMTGDVTLSPNASCL-------VMTTEILRGMLYRGSEV 179
L+ Q + E + + +G++ G + C+ + T L + R
Sbjct: 141 LAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFIT 200
Query: 180 LKEVAWVIFDEIHYMKD 196
++ +V+ DE M D
Sbjct: 201 FEDTRFVVLDEADRMLD 217
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 50/236 (21%), Positives = 89/236 (37%), Gaps = 37/236 (15%)
Query: 73 YSFEL-DPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKAL 131
Y FE Q+ ++ + + V+ + + GKTA ++ I +AL
Sbjct: 34 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLD-----IQVRETQAL 88
Query: 132 SNQKYRELHQEFKDVGLMTGDVTLSPNASCLVMTT--EILRGMLYRGSEVLKEVAWVIFD 189
REL + + L GD +C+ T E +R + Y G V+ +FD
Sbjct: 89 ILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFD 147
Query: 190 EIHYMKDRERGVV--------------WEESII----FLPPAIKMVFLSATMSNATQFAE 231
I R R + ++E I +LPPA ++V +SAT+ + + E
Sbjct: 148 MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH--EILE 205
Query: 232 WICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTF 287
P ++ ++ + G + V E+E+++ D L DT
Sbjct: 206 MTNKFMTDPIRIL--------VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 253
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 50/236 (21%), Positives = 89/236 (37%), Gaps = 37/236 (15%)
Query: 73 YSFEL-DPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKAL 131
Y FE Q+ ++ + + V+ + + GKTA ++ I +AL
Sbjct: 19 YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLD-----IQVRETQAL 73
Query: 132 SNQKYRELHQEFKDVGLMTGDVTLSPNASCLVMTT--EILRGMLYRGSEVLKEVAWVIFD 189
REL + + L GD +C+ T E +R + Y G V+ +FD
Sbjct: 74 ILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFD 132
Query: 190 EIHYMKDRERGVV--------------WEESII----FLPPAIKMVFLSATMSNATQFAE 231
I R R + ++E I +LPPA ++V +SAT+ + + E
Sbjct: 133 MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPH--EILE 190
Query: 232 WICHLHKQPCHVVYTDFRPTPLQHYVFPVGGSGLYLVVDEKEQFREDNFVKLQDTF 287
P ++ ++ + G + V E+E+++ D L DT
Sbjct: 191 MTNKFMTDPIRIL--------VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL 238
>pdb|4D93|A Chain A, Crystal Structure Of Tep1s
pdb|4D93|B Chain B, Crystal Structure Of Tep1s
pdb|4D93|C Chain C, Crystal Structure Of Tep1s
Length = 1323
Score = 30.4 bits (67), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 48/121 (39%), Gaps = 24/121 (19%)
Query: 17 LHVTGTPEEESTKKQRNLTRSCVHEVAVPSGYALTKDEAIHGTFANPV------YNGEMA 70
L V E T Q N+ + EV +PSGY + ++ T NP+ Y G
Sbjct: 1193 LRVCANYIPELTDSQSNM---ALIEVTLPSGYVVDRNPISEQTTVNPIQNMEIRYGGTSV 1249
Query: 71 KTY---------SFELDPFQRVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDKQR 121
Y F + ++R VA L+R V+V + + A+ Y + DKQ
Sbjct: 1250 VLYYYKMGTERNCFTVTAYRRFKVA-LKRPAYVVVYDYYNTNLNAIKVYEV-----DKQN 1303
Query: 122 V 122
V
Sbjct: 1304 V 1304
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.134 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,353,427
Number of Sequences: 62578
Number of extensions: 953815
Number of successful extensions: 2690
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2642
Number of HSP's gapped (non-prelim): 40
length of query: 931
length of database: 14,973,337
effective HSP length: 108
effective length of query: 823
effective length of database: 8,214,913
effective search space: 6760873399
effective search space used: 6760873399
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)