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= psy1089
(404 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 149 bits (376), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 79/181 (43%), Positives = 118/181 (65%), Gaps = 11/181 (6%)
Query: 184 MTNVTMVLRNIISHPYLI-NKPYRIV----DGK--KEMVCDENIVSSSGKMIVLNQLLHK 236
+ N+ L+ +HPYL N R++ DGK +E V ++ SSGKM++L+QLL +
Sbjct: 509 LLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVL-RGLIMSSGKMVLLDQLLTR 567
Query: 237 LKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNG--STEWG 294
LK+ H+ L+FS MV++L+ + + ++ N+ RL G++ + +R ++ FN S ++
Sbjct: 568 LKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDF- 626
Query: 295 VFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCIYRLVSHSTY 354
VFLLSTRAGG G+NL ADT +++DSDWNPQ D+QA AR HRIGQ V +YRLVS T
Sbjct: 627 VFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTV 686
Query: 355 Q 355
+
Sbjct: 687 E 687
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 1 MHNILKPFFLRRLKCDVNLNLPPKKTTVIDCPMVPAQELMYTKVLTK 47
+H ++PF LRRLK DV +LP K ++ + Q Y +LTK
Sbjct: 447 LHRRIQPFILRRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTK 493
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 99.8 bits (247), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 55/134 (41%), Positives = 82/134 (61%), Gaps = 2/134 (1%)
Query: 224 SGKMIVLNQLLHKLKQT-NHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERND 282
SGKM+VL+ +L + T + K ++ S + L+ E+LC Y Y RL G++ ++R
Sbjct: 398 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAK 457
Query: 283 AVQQFNG-STEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTK 341
V++FN S+ +F+LS++AGG GLNL A+ +++D DWNP D QA AR R GQ K
Sbjct: 458 IVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKK 517
Query: 342 PVCIYRLVSHSTYQ 355
IYRL+S T +
Sbjct: 518 TCYIYRLLSTGTIE 531
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 89.0 bits (219), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 56/186 (30%), Positives = 92/186 (49%), Gaps = 15/186 (8%)
Query: 172 NVDEILHHVNVKMTNVTMV-LRNIISHPYLINKPYRIVDGKKEMVCDENIVSSSGKMIVL 230
N+D + M T++ L+ I+ HP L+ E V SGKMI
Sbjct: 284 NIDSVTGIKRKGMILSTLLKLKQIVDHPALLK-------------GGEQSVRRSGKMIRT 330
Query: 231 NQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLE-NYNYYRLHGSIRNEERNDAVQQFNG 289
+++ + K +F+ V + I + E N L+G + +ER+D + +F
Sbjct: 331 MEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQN 390
Query: 290 STEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCIYRLV 349
+ +LS +AGG G+NLT+A+ I +D WNP V+ QA R +RIGQT+ V +++L+
Sbjct: 391 NPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLI 450
Query: 350 SHSTYQ 355
S T +
Sbjct: 451 SVGTLE 456
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 1 MHNILKPFFLRRLKCDVNL--NLPPKKTTVIDCPMVPAQELMY 41
+ I+ PF LRR K D + +LP K T + C + P Q MY
Sbjct: 232 LKAIISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMY 274
>pdb|1Z5Z|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal Domain
pdb|1Z5Z|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal Domain
Length = 271
Score = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 52/166 (31%), Positives = 84/166 (50%), Gaps = 14/166 (8%)
Query: 191 LRNIISHPYLINKPYRIVDGKKEMVCDENIVSSSGKMIVLNQLLHKLKQTNHKTLVFSTM 250
L+ I+ HP L+ E V SGKMI +++ + K +F+
Sbjct: 75 LKQIVDHPALLK-------------GGEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQF 121
Query: 251 VKVLNFIEELCVLE-NYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRAGGQGLNL 309
V + I + E N L+G + +ER+D + +F + +LS +AGG G+NL
Sbjct: 122 VDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINL 181
Query: 310 TAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCIYRLVSHSTYQ 355
T+A+ I +D WNP V+ QA R +RIGQT+ V +++L+S T +
Sbjct: 182 TSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLE 227
>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
pdb|1Z63|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
Length = 500
Score = 86.3 bits (212), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 51/166 (30%), Positives = 82/166 (49%), Gaps = 14/166 (8%)
Query: 191 LRNIISHPYLINKPYRIVDGKKEMVCDENIVSSSGKMIVLNQLLHKLKQTNHKTLVFSTM 250
L+ I+ HP L+ E V SGK I +++ + K +F+
Sbjct: 304 LKQIVDHPALLK-------------GGEQSVRRSGKXIRTXEIIEEALDEGDKIAIFTQF 350
Query: 251 VKVLNFIEELCVLE-NYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRAGGQGLNL 309
V I + E N L+G + +ER+D + +F + +LS +AGG G+NL
Sbjct: 351 VDXGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINL 410
Query: 310 TAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCIYRLVSHSTYQ 355
T+A+ I +D WNP V+ QA R +RIGQT+ V +++L+S T +
Sbjct: 411 TSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLE 456
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 1 MHNILKPFFLRRLKCDVNL--NLPPKKTTVIDCPMVPAQELMY 41
+ I+ PF LRR K D + +LP K T + C + P Q Y
Sbjct: 232 LKAIISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAXY 274
>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain
pdb|2P6N|B Chain B, Human Dead-box Rna Helicase Ddx41, Helicase Domain
Length = 191
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 54/120 (45%), Gaps = 11/120 (9%)
Query: 221 VSSSGKMIVLNQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEER 280
V KM+ L L L++T L+F+ ++ I E +L+ +HG EER
Sbjct: 37 VKEEAKMVYL---LECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEER 93
Query: 281 NDAVQQFNGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQT 340
A++ F + L++T +GL+ A I YD P+ + E HRIG+T
Sbjct: 94 TKAIEAFREGKKD--VLVATDVASKGLDFPAIQHVINYDM---PE---EIENYVHRIGRT 145
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 8/100 (8%)
Query: 244 TLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRAG 303
TLVF K + +E+ E Y +HG +R +A+ QF L++T
Sbjct: 279 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS--PILVATAVA 336
Query: 304 GQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPV 343
+GL+++ I +D + E HRIG+T V
Sbjct: 337 ARGLDISNVKHVINFD------LPSDIEEYVHRIGRTGRV 370
>pdb|2JGN|A Chain A, Ddx3 Helicase Domain
pdb|2JGN|B Chain B, Ddx3 Helicase Domain
pdb|2JGN|C Chain C, Ddx3 Helicase Domain
Length = 185
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 8/100 (8%)
Query: 244 TLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRAG 303
TLVF K + +E+ E Y +HG +R +A+ QF L++T
Sbjct: 49 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGK--SPILVATAVA 106
Query: 304 GQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPV 343
+GL+++ I +D + E HRIG+T V
Sbjct: 107 ARGLDISNVKHVINFD------LPSDIEEYVHRIGRTGRV 140
>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 52/113 (46%), Gaps = 21/113 (18%)
Query: 236 KLKQTNHKTLVFSTMVKVLNFIEELC-VLEN-----YNYYRLHGSIRNEERNDAVQQFNG 289
K + +N+K ++F+ VK +F LC +L+N HG I +R V++F
Sbjct: 28 KERDSNYKAIIFAPTVKFTSF---LCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFK- 83
Query: 290 STEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEAR--CHRIGQT 340
E G+ L+ T G +G++ + Q+ + +E HRIG+T
Sbjct: 84 KDESGI-LVCTDVGARGMDFPNVHEVL--------QIGVPSELANYIHRIGRT 127
>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
Length = 256
Score = 34.7 bits (78), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 52/113 (46%), Gaps = 21/113 (18%)
Query: 236 KLKQTNHKTLVFSTMVKVLNFIEELC-VLEN-----YNYYRLHGSIRNEERNDAVQQFNG 289
K + +N+K ++F+ VK +F LC +L+N HG I +R V++F
Sbjct: 28 KERDSNYKAIIFAPTVKFTSF---LCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFK- 83
Query: 290 STEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEAR--CHRIGQT 340
E G+ L+ T G +G++ + Q+ + +E HRIG+T
Sbjct: 84 KDESGI-LVCTDVGARGMDFPNVHEVL--------QIGVPSELANYIHRIGRT 127
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 34.7 bits (78), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 52/113 (46%), Gaps = 21/113 (18%)
Query: 236 KLKQTNHKTLVFSTMVKVLNFIEELC-VLEN-----YNYYRLHGSIRNEERNDAVQQFNG 289
K + +N+K ++F+ VK +F LC +L+N HG I +R V++F
Sbjct: 28 KERDSNYKAIIFAPTVKFTSF---LCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFK- 83
Query: 290 STEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEAR--CHRIGQT 340
E G+ L+ T G +G++ + Q+ + +E HRIG+T
Sbjct: 84 KDESGI-LVCTDVGARGMDFPNVHEVL--------QIGVPSELANYIHRIGRT 127
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 34.7 bits (78), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 53/116 (45%), Gaps = 27/116 (23%)
Query: 236 KLKQTNHKTLVFSTMVKVLNFI---------EELCVLENYNYYRLHGSIRNEERNDAVQQ 286
K + +N+K ++F+ VK +F+ ++L +LE HG I +R V++
Sbjct: 283 KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILE------FHGKITQNKRTSLVKR 336
Query: 287 FNGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEAR--CHRIGQT 340
F E G+ L+ T G +G++ + Q+ + +E HRIG+T
Sbjct: 337 FK-KDESGI-LVCTDVGARGMDFPNVHEVL--------QIGVPSELANYIHRIGRT 382
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 53/116 (45%), Gaps = 27/116 (23%)
Query: 236 KLKQTNHKTLVFSTMVKVLNFI---------EELCVLENYNYYRLHGSIRNEERNDAVQQ 286
K + +N+K ++F+ VK +F+ ++L +LE HG I +R V++
Sbjct: 283 KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILE------FHGKITQNKRTSLVKR 336
Query: 287 FNGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEAR--CHRIGQT 340
F E G+ L+ T G +G++ + Q+ + +E HRIG+T
Sbjct: 337 FK-KDESGI-LVCTDVGARGMDFPNVHEVL--------QIGVPSELANYIHRIGRT 382
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 53/116 (45%), Gaps = 27/116 (23%)
Query: 236 KLKQTNHKTLVFSTMVKVLNFI---------EELCVLENYNYYRLHGSIRNEERNDAVQQ 286
K + +N+K ++F+ VK +F+ ++L +LE HG I +R V++
Sbjct: 334 KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILE------FHGKITQNKRTSLVKR 387
Query: 287 FNGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEAR--CHRIGQT 340
F E G+ L+ T G +G++ + Q+ + +E HRIG+T
Sbjct: 388 FK-KDESGI-LVCTDVGARGMDFPNVHEVL--------QIGVPSELANYIHRIGRT 433
>pdb|3DMQ|A Chain A, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
pdb|3DMQ|B Chain B, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
Length = 968
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 29/68 (42%)
Query: 279 ERNDAVQQFNGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIG 338
ER+ A F LL + G +G N A + +D +NP + Q R RIG
Sbjct: 542 ERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRIG 601
Query: 339 QTKPVCIY 346
Q + I+
Sbjct: 602 QAHDIQIH 609
>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 = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 27/114 (23%), Positives = 51/114 (44%), Gaps = 10/114 (8%)
Query: 231 NQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQF-NG 289
++L+ L + T+VF + +F+ + + +HG +R A++ F NG
Sbjct: 290 SKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNG 349
Query: 290 STEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPV 343
S + L++T +GL++ I YD + + + HRIG+T V
Sbjct: 350 SMKV---LIATSVASRGLDIKNIKHVINYD------MPSKIDDYVHRIGRTGRV 394
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 3/104 (2%)
Query: 242 HKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTR 301
++ ++F V+ + +L V +N+ +H + EER QQF L++T
Sbjct: 250 NQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR--ILVATN 307
Query: 302 AGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
G+G+++ + YD + + AR R G TK + I
Sbjct: 308 LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG-TKGLAI 350
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 3/104 (2%)
Query: 242 HKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTR 301
++ ++F V+ + +L V +N+ +H + EER QQF L++T
Sbjct: 251 NQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR--ILVATN 308
Query: 302 AGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
G+G+++ + YD + + AR R G TK + I
Sbjct: 309 LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG-TKGLAI 351
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 3/104 (2%)
Query: 242 HKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTR 301
++ ++F V+ + +L V +N+ +H + EER QQF L++T
Sbjct: 251 NQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR--ILVATN 308
Query: 302 AGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
G+G+++ + YD + + AR R G TK + I
Sbjct: 309 LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG-TKGLAI 351
>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 = 32.0 bits (71), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 3/106 (2%)
Query: 240 TNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLS 299
T + ++F + ++++ E N+ +HG + +ER +++F L+S
Sbjct: 254 TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLIS 311
Query: 300 TRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
T +GL++ I YD N ++ I R R G+ K V I
Sbjct: 312 TDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR-KGVAI 356
>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 = 0.63, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 46/103 (44%), Gaps = 3/103 (2%)
Query: 243 KTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRA 302
+ ++F + ++++ E N+ +HG + +ER +++F L+ST
Sbjct: 279 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDV 336
Query: 303 GGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
+GL++ I YD N ++ I R R G+ K V I
Sbjct: 337 WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR-KGVAI 378
>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 = 0.65, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 46/103 (44%), Gaps = 3/103 (2%)
Query: 243 KTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRA 302
+ ++F + ++++ E N+ +HG + +ER +++F L+ST
Sbjct: 279 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDV 336
Query: 303 GGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
+GL++ I YD N ++ I R R G+ K V I
Sbjct: 337 WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR-KGVAI 378
>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 = 0.66, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 46/103 (44%), Gaps = 3/103 (2%)
Query: 243 KTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRA 302
+ ++F + ++++ E N+ +HG + +ER +++F L+ST
Sbjct: 278 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDV 335
Query: 303 GGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
+GL++ I YD N ++ I R R G+ K V I
Sbjct: 336 WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR-KGVAI 377
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 32.0 bits (71), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 3/104 (2%)
Query: 242 HKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTR 301
++ ++F V+ + +L V +N+ +H + EER QQF L++T
Sbjct: 32 NQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR--ILVATN 89
Query: 302 AGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQTKPVCI 345
G+G+++ + YD + + AR R G TK + I
Sbjct: 90 LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG-TKGLAI 132
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 2/97 (2%)
Query: 243 KTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRA 302
+ ++F + ++++ E N+ +HG + +ER +++F L+ST
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDV 299
Query: 303 GGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQ 339
+GL++ I YD N ++ I R R G+
Sbjct: 300 WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR 336
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 2/97 (2%)
Query: 243 KTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLSTRA 302
+ ++F + ++++ E N+ +HG + +ER +++F L+ST
Sbjct: 242 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDV 299
Query: 303 GGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQ 339
+GL++ I YD N ++ I R R G+
Sbjct: 300 WARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR 336
>pdb|3MTN|A Chain A, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
pdb|3MTN|C Chain C, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
Length = 373
Score = 31.2 bits (69), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 94 KAGKREQTIDSNQLVQQPKRRKCSLNKTYDLTEIDR---MFDSMIERDDTSDTEV---QV 147
+ G+R I +N V P RR +L + +L++ DR M+ +ER+D+ ++ Q+
Sbjct: 130 RRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQL 189
Query: 148 EDKIKVEPCENSSNAQDV 165
+ +K + C S +V
Sbjct: 190 KSCLKCQACGYRSTTFEV 207
>pdb|2Y5B|A Chain A, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
pdb|2Y5B|E Chain E, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
Length = 370
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 94 KAGKREQTIDSNQLVQQPKRRKCSLNKTYDLTEIDR---MFDSMIERDDTSDTEV---QV 147
+ G+R I +N V P RR +L + +L++ DR M+ +ER+D+ ++ Q+
Sbjct: 124 RRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQL 183
Query: 148 EDKIKVEPCENSSNAQDV 165
+ +K + C S +V
Sbjct: 184 KSCLKCQACGYRSTTFEV 201
>pdb|3I3T|A Chain A, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|C Chain C, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|E Chain E, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|G Chain G, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
Length = 355
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 94 KAGKREQTIDSNQLVQQPKRRKCSLNKTYDLTEIDR---MFDSMIERDDTSDTEV---QV 147
+ G+R I +N V P RR +L + +L++ DR M+ +ER+D+ ++ Q+
Sbjct: 111 RRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQL 170
Query: 148 EDKIKVEPCENSSNAQDV 165
+ +K + C S +V
Sbjct: 171 KSCLKCQACGYRSTTFEV 188
>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAX|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
Length = 193
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 57/121 (47%), Gaps = 12/121 (9%)
Query: 221 VSSSGKMIVLNQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEER 280
V+ K+ LN L +L Q N ++++F + + + + Y+ + +H +R E R
Sbjct: 26 VTERQKVHCLNTLFSRL-QIN-QSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHR 83
Query: 281 NDAVQQF-NGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQ 339
N F NG L+ T +G+++ A + I +D P++ AE HRIG+
Sbjct: 84 NRVFHDFRNGLCRN---LVCTDLFTRGIDIQAVNVVINFDF---PKL---AETYLHRIGR 134
Query: 340 T 340
+
Sbjct: 135 S 135
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 244 TLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFN-GSTEWGVFLLSTRA 302
+++F K N + E + LHG ++ +ER+ + F G ++ L++T
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNV 302
Query: 303 GGQGLNLTAADTCILYD--SDWNPQVDIQAEARCHRIGQT 340
+G+++ + YD + N Q D HRIG+T
Sbjct: 303 LARGIDIPTVSMVVNYDLPTLANGQAD--PATYIHRIGRT 340
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 244 TLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFN-GSTEWGVFLLSTRA 302
+++F K N + E + LHG ++ +ER+ + F G ++ L++T
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNV 302
Query: 303 GGQGLNLTAADTCILYD--SDWNPQVDIQAEARCHRIGQT 340
+G+++ + YD + N Q D HRIG+T
Sbjct: 303 LARGIDIPTVSMVVNYDLPTLANGQAD--PATYIHRIGRT 340
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 244 TLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFN-GSTEWGVFLLSTRA 302
+++F K N + E + LHG ++ +ER+ + F G ++ L++T
Sbjct: 38 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNV 94
Query: 303 GGQGLNLTAADTCILYD--SDWNPQVDIQAEARCHRIGQT 340
+G+++ + YD + N Q D HRIG+T
Sbjct: 95 LARGIDIPTVSMVVNYDLPTLANGQAD--PATYIHRIGRT 132
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 244 TLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFN-GSTEWGVFLLSTRA 302
+++F K N + E + LHG ++ +ER+ + F G ++ L++T
Sbjct: 40 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNV 96
Query: 303 GGQGLNLTAADTCILYD--SDWNPQVDIQAEARCHRIGQT 340
+G+++ + YD + N Q D HRIG+T
Sbjct: 97 LARGIDIPTVSXVVNYDLPTLANGQAD--PATYIHRIGRT 134
>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
H337r And Ip6
pdb|3PEV|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
And Ip6
Length = 188
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 244 TLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFN-GSTEWGVFLLSTRA 302
+++F K N + E + LHG ++ +ER+ + F G ++ L++T
Sbjct: 39 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNV 95
Query: 303 GGQGLNLTAADTCILYD--SDWNPQVDIQAEARCHRIGQT 340
+G+++ + YD + N Q D HRIG+T
Sbjct: 96 LARGIDIPTVSXVVNYDLPTLANGQAD--PATYIHRIGRT 133
>pdb|3PDM|P Chain P, Hibiscus Latent Singapore Virus
Length = 162
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 22/105 (20%)
Query: 88 SNASSVKAGK---REQTIDSNQLVQQPKRRKCSLNKTYDL---------TEIDRMFDSMI 135
SN+ +AG+ REQ I+S Q+V +LN Y L + +F++++
Sbjct: 32 SNSFQTQAGRDTLREQLINSLQIV-------ANLNTRYPLLGFYVWVRNPTLAPVFEALL 84
Query: 136 ERDDTSDTEVQVEDKIKVEPCENSSNAQ---DVPSAEEKNVDEIL 177
DT + ++VE++ + E + Q D A K +D IL
Sbjct: 85 RATDTKNRIIEVEEESRPTTAETLNATQRVDDATVAIHKEIDNIL 129
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 28.5 bits (62), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 10/105 (9%)
Query: 240 TNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLS 299
T + ++F K +++ E + L G + E+R +++F E L++
Sbjct: 281 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK--VLVT 338
Query: 300 TRAGGQGLNLTAADTCILYD----SDWNPQVDIQAEARCHRIGQT 340
T +G+++ I +D D NP E HRIG+T
Sbjct: 339 TNVCARGIDVEQVSVVINFDLPVDKDGNPD----NETYLHRIGRT 379
>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
pdb|3FHT|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
Length = 412
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 10/105 (9%)
Query: 240 TNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLS 299
T + ++F K +++ E + L G + E+R +++F E L++
Sbjct: 265 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK--VLVT 322
Query: 300 TRAGGQGLNLTAADTCILYD----SDWNPQVDIQAEARCHRIGQT 340
T +G+++ I +D D NP E HRIG+T
Sbjct: 323 TNVCARGIDVEQVSVVINFDLPVDKDGNPD----NETYLHRIGRT 363
>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
pdb|3EWS|B Chain B, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
Length = 445
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 10/105 (9%)
Query: 240 TNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLS 299
T + ++F K +++ E + L G + E+R +++F E L++
Sbjct: 302 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK--VLVT 359
Query: 300 TRAGGQGLNLTAADTCILYD----SDWNPQVDIQAEARCHRIGQT 340
T +G+++ I +D D NP E HRIG+T
Sbjct: 360 TNVCARGIDVEQVSVVINFDLPVDKDGNPD----NETYLHRIGRT 400
>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|D Chain D, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 479
Score = 28.1 bits (61), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 10/105 (9%)
Query: 240 TNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEERNDAVQQFNGSTEWGVFLLS 299
T + ++F K +++ E + L G + E+R +++F E L++
Sbjct: 332 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKE--KVLVT 389
Query: 300 TRAGGQGLNLTAADTCILYD----SDWNPQVDIQAEARCHRIGQT 340
T +G+++ I +D D NP E HRIG+T
Sbjct: 390 TNVCARGIDVEQVSVVINFDLPVDKDGNPD----NETYLHRIGRT 430
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 53/121 (43%), Gaps = 12/121 (9%)
Query: 221 VSSSGKMIVLNQLLHKLKQTNHKTLVFSTMVKVLNFIEELCVLENYNYYRLHGSIRNEER 280
V K+ LN L KL Q N + ++F + + + Y+ Y H ++ +ER
Sbjct: 240 VEERQKLHCLNTLFSKL-QIN-QAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQER 297
Query: 281 NDAVQQF-NGSTEWGVFLLSTRAGGQGLNLTAADTCILYDSDWNPQVDIQAEARCHRIGQ 339
N +F G L+ + +G+++ A + I +D P+ AE HRIG+
Sbjct: 298 NKVFHEFRQGKVRT---LVCSDLLTRGIDIQAVNVVINFDF---PKT---AETYLHRIGR 348
Query: 340 T 340
+
Sbjct: 349 S 349
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 0.133 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,400,130
Number of Sequences: 62578
Number of extensions: 377638
Number of successful extensions: 819
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 789
Number of HSP's gapped (non-prelim): 58
length of query: 404
length of database: 14,973,337
effective HSP length: 101
effective length of query: 303
effective length of database: 8,652,959
effective search space: 2621846577
effective search space used: 2621846577
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: 53 (25.0 bits)