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= 000642
(1377 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 = 216 bits (549), Expect = 9e-56, Method: Compositional matrix adjust.
Identities = 118/330 (35%), Positives = 190/330 (57%), Gaps = 19/330 (5%)
Query: 426 TVQTPELFKGSLKEYQLKGLQWLVNCYEQGLNGILADEMGLGKTIQAMAFLAHLAEEKNI 485
+VQ P + G L+++QL G+ W+ + +G NGILADEMGLGKT+Q +AF++ L +
Sbjct: 226 SVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQ 285
Query: 486 WGPFLVVAPASVLNNWADEISRFCPDLKTLPYWGGLQERMVLRK---NINPKRLYRRDAG 542
GP ++V P S + W D ++ PDL + Y G + R +R+ NP+ ++
Sbjct: 286 NGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMK 345
Query: 543 FHILITSYQLLVADEKYFRRVKWQYMVLDEAQAIKSSNSIRWKTLLSFNCRNRLLLTGTP 602
F++L+T+Y+ ++ D +KWQ+M +DEA +K++ S +++L SF NR+L+TGTP
Sbjct: 346 FNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTP 405
Query: 603 IQNNMAELWALLHFIMPTLFDSHEQFNEWFSKGIESHAEHGGTLNEHQLNRLHAILKPFM 662
+QNN+ EL AL++F+MP F ++ + F E E+ ++ LH ++PF+
Sbjct: 406 LQNNIKELAALVNFLMPGRFTIDQEID--FENQDEEQEEY--------IHDLHRRIQPFI 455
Query: 663 LRRVKKDVISELTTKTEVMVHCKLSSRQQAFYQAIKNKISLAGLFDNSRGHLNEKKILNL 722
LRR+KKDV L +KTE ++ +LS Q +Y+ I K A GH +L
Sbjct: 456 LRRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGH------FSL 509
Query: 723 MNIVIQLRKVCNHPELFERNEGSSYLYFGE 752
+NI+ +L+K NHP LF+ E FG+
Sbjct: 510 LNIMNELKKASNHPYLFDNAEERVLQKFGD 539
Score = 167 bits (423), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 83/163 (50%), Positives = 114/163 (69%), Gaps = 1/163 (0%)
Query: 1051 LLTDSGKLQTLDILLKRLRAENHRVLLFAQMTKMLNILEDYMNYRKYRYLRLDGSSTIMD 1110
L+ SGK+ LD LL RL+ + HRVL+F+QM +ML+IL DY++ + + RLDG+
Sbjct: 551 LIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQ 610
Query: 1111 RRDMVRDFQH-RSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRLG 1169
RR + F S+ FVFLLSTRAGGLGINL ADTV+ ++SDWNP DLQAM RAHR+G
Sbjct: 611 RRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIG 670
Query: 1170 QTKDVTVYRLICKETVEEKILQRASQKNTVQQLVMTGGHVQGD 1212
Q V VYRL+ K+TVEE++L+RA +K ++ +++ G G+
Sbjct: 671 QKNHVMVYRLVSKDTVEEEVLERARKKMILEYAIISLGVTDGN 713
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 172 bits (435), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 102/318 (32%), Positives = 176/318 (55%), Gaps = 30/318 (9%)
Query: 430 PELFKGSLKEYQLKGLQWLVNCYEQGLNGILADEMGLGKTIQAMAFLAHLAEEKNIWGPF 489
P K +L+ YQ+KG W+ + G LAD+MGLGKT+Q +A + A+++N P
Sbjct: 31 PYNIKANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSD-AKKENELTPS 89
Query: 490 LVVAPASVLNNWADEISRFCPDLKTLPYWGGLQERMVLRKNINPKRLYRRDAGFHILITS 549
LV+ P SVL NW +E+S+F P L+ + + R + + I++T+
Sbjct: 90 LVICPLSVLKNWEEELSKFAPHLRFAVF--------------HEDRSKIKLEDYDIILTT 135
Query: 550 YQLLVADEKYFRRVKWQYMVLDEAQAIKSSNSIRWKTLLSFNCRNRLLLTGTPIQNNMAE 609
Y +L+ D + + V+W+Y+V+DEAQ IK+ + +K + + R+ LTGTPI+N + +
Sbjct: 136 YAVLLRDTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDD 194
Query: 610 LWALLHFIMPTLFDSHEQFNEWFSKGIESHAEHGGTLNEHQLNRLHAILKPFMLRRVKKD 669
LW+++ F+ P L S+ +F F+ I + G + + + L AI+ PF+LRR K D
Sbjct: 195 LWSIMTFLNPGLLGSYSEFKSKFATPI----KKGDNMAKEE---LKAIISPFILRRTKYD 247
Query: 670 --VISELTTKTEVMVHCKLSSRQQAFYQAIKNKISLAGLFDNSRGHLNEKKILNLMNIVI 727
+I++L K E V+C L+ Q A Y+A + LF+N K+ +++ ++
Sbjct: 248 KAIINDLPDKIETNVYCNLTPEQAAMYKA-----EVENLFNNIDSVTGIKRKGMILSTLL 302
Query: 728 QLRKVCNHPELFERNEGS 745
+L+++ +HP L + E S
Sbjct: 303 KLKQIVDHPALLKGGEQS 320
Score = 92.0 bits (227), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 56/159 (35%), Positives = 96/159 (60%), Gaps = 11/159 (6%)
Query: 1055 SGKL-QTLDILLKRLRAENHRVLLFAQMTKM----LNILEDYMNYR-KYRYLRLDGSSTI 1108
SGK+ +T++I+ + L E ++ +F Q M NI+E +N + Y G +
Sbjct: 324 SGKMIRTMEIIEEALD-EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLY----GELSK 378
Query: 1109 MDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRL 1168
+R D++ FQ+ + +LS +AGG GINLT+A+ VI ++ WNP ++ QA DR +R+
Sbjct: 379 KERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI 438
Query: 1169 GQTKDVTVYRLICKETVEEKILQRASQKNTVQQLVMTGG 1207
GQT++V V++LI T+EEKI Q + K ++ + +++ G
Sbjct: 439 GQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSG 477
>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 = 165 bits (418), Expect = 1e-40, Method: Compositional matrix adjust.
Identities = 100/318 (31%), Positives = 170/318 (53%), Gaps = 30/318 (9%)
Query: 430 PELFKGSLKEYQLKGLQWLVNCYEQGLNGILADEMGLGKTIQAMAFLAHLAEEKNIWGPF 489
P K +L+ YQ+KG W + G LAD+ GLGKT+Q +A + A+++N P
Sbjct: 31 PYNIKANLRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSD-AKKENELTPS 89
Query: 490 LVVAPASVLNNWADEISRFCPDLKTLPYWGGLQERMVLRKNINPKRLYRRDAGFHILITS 549
LV+ P SVL NW +E+S+F P L+ + + R + + I++T+
Sbjct: 90 LVICPLSVLKNWEEELSKFAPHLRFAVF--------------HEDRSKIKLEDYDIILTT 135
Query: 550 YQLLVADEKYFRRVKWQYMVLDEAQAIKSSNSIRWKTLLSFNCRNRLLLTGTPIQNNMAE 609
Y +L+ D + + V+W+Y+V+DEAQ IK+ + +K + + R+ LTGTPI+N + +
Sbjct: 136 YAVLLRDTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDD 194
Query: 610 LWALLHFIMPTLFDSHEQFNEWFSKGIESHAEHGGTLNEHQLNRLHAILKPFMLRRVKKD 669
LW++ F+ P L S+ +F F+ I+ + L AI+ PF+LRR K D
Sbjct: 195 LWSIXTFLNPGLLGSYSEFKSKFATPIKKG-------DNXAKEELKAIISPFILRRTKYD 247
Query: 670 --VISELTTKTEVMVHCKLSSRQQAFYQAIKNKISLAGLFDNSRGHLNEKKILNLMNIVI 727
+I++L K E V+C L+ Q A Y+A + LF+N K+ +++ ++
Sbjct: 248 KAIINDLPDKIETNVYCNLTPEQAAXYKA-----EVENLFNNIDSVTGIKRKGXILSTLL 302
Query: 728 QLRKVCNHPELFERNEGS 745
+L+++ +HP L + E S
Sbjct: 303 KLKQIVDHPALLKGGEQS 320
Score = 89.7 bits (221), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/159 (34%), Positives = 95/159 (59%), Gaps = 11/159 (6%)
Query: 1055 SGK-LQTLDILLKRLRAENHRVLLFAQMTK----MLNILEDYMNYR-KYRYLRLDGSSTI 1108
SGK ++T +I+ + L E ++ +F Q + NI+E +N + Y G +
Sbjct: 324 SGKXIRTXEIIEEAL-DEGDKIAIFTQFVDXGKIIRNIIEKELNTEVPFLY----GELSK 378
Query: 1109 MDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRL 1168
+R D++ FQ+ + +LS +AGG GINLT+A+ VI ++ WNP ++ QA DR +R+
Sbjct: 379 KERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI 438
Query: 1169 GQTKDVTVYRLICKETVEEKILQRASQKNTVQQLVMTGG 1207
GQT++V V++LI T+EEKI Q + K ++ + +++ G
Sbjct: 439 GQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSG 477
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 117 bits (293), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 61/152 (40%), Positives = 92/152 (60%), Gaps = 2/152 (1%)
Query: 1055 SGKLQTLDILLKRLRAE-NHRVLLFAQMTKMLNILEDYMNYRKYRYLRLDGSSTIMDRRD 1113
SGK+ LD +L R + +V+L + T+ L++ E R+Y Y+RLDG+ +I R
Sbjct: 398 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAK 457
Query: 1114 MVRDFQHRSDI-FVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRLGQTK 1172
+V F + S F+F+LS++AGG G+NL A+ ++ ++ DWNP D QAM R R GQ K
Sbjct: 458 IVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKK 517
Query: 1173 DVTVYRLICKETVEEKILQRASQKNTVQQLVM 1204
+YRL+ T+EEKILQR + K + V+
Sbjct: 518 TCYIYRLLSTGTIEEKILQRQAHKKALSSCVV 549
Score = 105 bits (263), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 89/338 (26%), Positives = 166/338 (49%), Gaps = 32/338 (9%)
Query: 421 MPVTSTVQTPELFKGSLKEYQLKGLQWLVNCY-----EQGLNGILADEMGLGKTIQAMAF 475
+PV V P L K L+ +Q +G+++L +C E I+ADEMGLGKT+Q +
Sbjct: 42 LPVHVVVD-PVLSK-VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITL 99
Query: 476 LAHLAEEKNIWGP----FLVVAPASVLNNWADEISRFCPD-LKTLPYWGGLQERMVLRKN 530
+ L ++ P +VV+P+S++ NW +E+ ++ ++ + GG ++ + K
Sbjct: 100 IWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDE-IDSKL 158
Query: 531 INPKRLYRRDAGFHI----LITSYQLLVADEKYFRRVKWQYMVLDEAQAIKSSNSIRWKT 586
+N + G I LI SY+ + + K ++ DE +K+S++ +
Sbjct: 159 VN----FISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLA 214
Query: 587 LLSFNCRNRLLLTGTPIQNNMAELWALLHFIMPTLFDSHEQFNEWFS----KGIESHA-E 641
L S N + R+L++GTPIQN++ E ++L+HF+ + + ++F + F KG ++ A +
Sbjct: 215 LNSMNAQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASD 274
Query: 642 HGGTLNEHQLNRLHAILKPFMLRRVKKDVISELTTKTEVMVHCKLSSRQQAFYQAIKNKI 701
E +L L +I+ ++RR + L K E +V C L+ Q+ Y+ +
Sbjct: 275 KDRAAGEQKLQELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQA 334
Query: 702 SLAGLFDNSRGHLNEKKILNLMNIVIQLRKVCNHPELF 739
K ++ ++ + L+K+CNHP L
Sbjct: 335 KPVESLQTG------KISVSSLSSITSLKKLCNHPALI 366
>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 = 91.7 bits (226), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 56/159 (35%), Positives = 96/159 (60%), Gaps = 11/159 (6%)
Query: 1055 SGKL-QTLDILLKRLRAENHRVLLFAQMTKM----LNILEDYMNYRK-YRYLRLDGSSTI 1108
SGK+ +T++I+ + L E ++ +F Q M NI+E +N + Y G +
Sbjct: 95 SGKMIRTMEIIEEAL-DEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLY----GELSK 149
Query: 1109 MDRRDMVRDFQHRSDIFVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRL 1168
+R D++ FQ+ + +LS +AGG GINLT+A+ VI ++ WNP ++ QA DR +R+
Sbjct: 150 KERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI 209
Query: 1169 GQTKDVTVYRLICKETVEEKILQRASQKNTVQQLVMTGG 1207
GQT++V V++LI T+EEKI Q + K ++ + +++ G
Sbjct: 210 GQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSG 248
Score = 37.0 bits (84), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 672 SELTTKTEVMVHCKLSSRQQAFYQAIKNKISLAGLFDNSRGHLNEKKILNLMNIVIQLRK 731
S+L K E V+C L+ Q A Y+A + LF+N K+ +++ +++L++
Sbjct: 23 SDLPDKIETNVYCNLTPEQAAMYKA-----EVENLFNNIDSVTGIKRKGMILSTLLKLKQ 77
Query: 732 VCNHPELFERNEGS 745
+ +HP L + E S
Sbjct: 78 IVDHPALLKGGEQS 91
>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 = 38.5 bits (88), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 48/188 (25%), Positives = 76/188 (40%), Gaps = 33/188 (17%)
Query: 459 ILADEMGLGKTIQAMAFLAHLAEEKNIWGPFLVVAPASVLNNWADEISRFCPDLKTLPYW 518
+LADE+GLGKTI+A L H L++ P ++ + W E R
Sbjct: 174 LLADEVGLGKTIEAGXIL-HQQLLSGAAERVLIIVPETLQHQWLVEXLR----------- 221
Query: 519 GGLQERMVLRKNI-NPKRLYRRDAGFHILITSYQLLVADEKYFRRVK----------WQY 567
R LR + + +R + + QL++ + RR K W
Sbjct: 222 -----RFNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDL 276
Query: 568 MVLDEAQAI---KSSNSIRWKTL--LSFNCRNRLLLTGTPIQNNMAELWALLHFIMPTLF 622
+V+DEA + + + S ++ + L+ + LLLT TP Q +A L + P F
Sbjct: 277 LVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLRLLDPNRF 336
Query: 623 DSHEQFNE 630
QF E
Sbjct: 337 HDFAQFVE 344
Score = 30.4 bits (67), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 1128 LLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRLGQTKDVTVY 1177
LL + G G N A + ++ +NP L Q + R R+GQ D+ ++
Sbjct: 560 LLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRIGQAHDIQIH 609
>pdb|1XMX|A Chain A, Crystal Structure Of Protein Vc1899 From Vibrio Cholerae
Length = 385
Score = 33.5 bits (75), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 4/97 (4%)
Query: 774 RNPIEYKIPKIVHQEILQSSEILCSAVGHGISRELFQKRFNIFSAENVYQSIFSLASGSD 833
++P+ P + H+ + S I+ +G ++Q+ ++ + N+ F + +GS+
Sbjct: 12 QDPVRLVTPLLDHRTV--SRHIIF--IGDHTQTVIYQRLSDVLNKRNISTDFFEIPAGSN 67
Query: 834 ASPVKSETFGFTHLMDLSPAEVAFLAKGSFMERLLFA 870
S +KS + EV F A RLL A
Sbjct: 68 TSAIKSAIRELAETLKARGEEVKFNASCGLRHRLLSA 104
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 32.3 bits (72), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 8/99 (8%)
Query: 1076 LLFAQMTKMLNILEDYMNYRKYRYLRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGG 1135
L+F + K + LED++ + Y + G + DR + + F RS L++T
Sbjct: 280 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQF--RSGKSPILVATAVAA 337
Query: 1136 LGINLTAADTVIFYESDWNPTLDLQAMDRAHRLGQTKDV 1174
G++++ VI N L + HR+G+T V
Sbjct: 338 RGLDISNVKHVI------NFDLPSDIEEYVHRIGRTGRV 370
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 465 GLGKTIQAMAFLAHLAEEKNIWGPFLVVAPASV 497
G GKT+ + + HLA + N GP LV AP+++
Sbjct: 381 GTGKTVTSATIVYHLARQGN--GPVLVCAPSNI 411
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 32.0 bits (71), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 465 GLGKTIQAMAFLAHLAEEKNIWGPFLVVAPASV 497
G GKT+ + + HLA + N GP LV AP+++
Sbjct: 205 GTGKTVTSATIVYHLARQGN--GPVLVCAPSNI 235
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 32.0 bits (71), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 465 GLGKTIQAMAFLAHLAEEKNIWGPFLVVAPASV 497
G GKT+ + + HLA + N GP LV AP+++
Sbjct: 204 GTGKTVTSATIVYHLARQGN--GPVLVCAPSNI 234
>pdb|2WSK|A Chain A, Crystal Structure Of Glycogen Debranching Enzyme Glgx From
Escherichia Coli K-12
Length = 657
Score = 31.6 bits (70), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 1023 LPVAKPALQLTYQIFGSCPPMQS--FDPAKLLTD 1054
LP A+P L+ Y++ G P + F+PAKLL D
Sbjct: 61 LPDARPGLRYGYRVHGPWQPAEGHRFNPAKLLID 94
>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 = 31.6 bits (70), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 8/99 (8%)
Query: 1076 LLFAQMTKMLNILEDYMNYRKYRYLRLDGSSTIMDRRDMVRDFQHRSDIFVFLLSTRAGG 1135
L+F + K + LED++ + Y + G + DR + + F RS L++T
Sbjct: 50 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQF--RSGKSPILVATAVAA 107
Query: 1136 LGINLTAADTVIFYESDWNPTLDLQAMDRAHRLGQTKDV 1174
G++++ VI N L + HR+G+T V
Sbjct: 108 RGLDISNVKHVI------NFDLPSDIEEYVHRIGRTGRV 140
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain
Length = 494
Score = 30.0 bits (66), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 1125 FVFLLSTRAGGLGINLTAADTVIFYESDWNPTLDLQAMDRAHRLGQTKDVTVYRLICKET 1184
F L++T G G+++ D V+FYE P+ ++++ R R G+ V L+ K T
Sbjct: 420 FNVLVATSVGEEGLDVPEVDLVVFYEP--VPS-AIRSIQRRGRTGRHMPGRVIILMAKGT 476
Query: 1185 VEEKILQRASQKNTVQQ 1201
+E + QK + Q
Sbjct: 477 RDEAYYWSSRQKEKIMQ 493
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
0.318 0.134 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 37,166,081
Number of Sequences: 62578
Number of extensions: 1482386
Number of successful extensions: 3163
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 3128
Number of HSP's gapped (non-prelim): 24
length of query: 1377
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1266
effective length of database: 8,027,179
effective search space: 10162408614
effective search space used: 10162408614
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)