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= psy3251
(959 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 1285 bits (3324), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 608/852 (71%), Positives = 690/852 (80%), Gaps = 55/852 (6%)
Query: 97 LPPHACKYCGIHDPAYVIMCNICKKWFCNGRGHTSGSHIINHLVRAKHKEVTLHKDGPLG 156
LP HAC YCGIHDPA V+ CN KKWFCNGRG+TSGSHI+NHLVRAK KEVTLHKDGPLG
Sbjct: 4 LPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLG 63
Query: 157 ETVLECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQNSLKDMNWDQEQWKPLIADRS 216
ETVLECY CG RN+F+LGFIPAKADSVVVLLCR PCA+Q+SLKD+NWD QW+PLI DR
Sbjct: 64 ETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRC 123
Query: 217 FLSWLVKVPTEQEQQRGRQVTSAQIAKLEEVWKDNAEATFQDLEKPGVDEDPHQVLLRYE 276
FLSWLVK+P+EQEQ R RQ+T+ QI KLEE+WK+N AT +DLEKPGVDE+P
Sbjct: 124 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEP-------- 175
Query: 277 DGYQYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDGYQY 336
++V +R++ D YQY
Sbjct: 176 -----------------------------QHVLLRYE------------------DAYQY 188
Query: 337 QNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDMRLMQGDEL 396
QNIFGPLVKLEADYDK+LKESQTQ+N+TVRWD+GLNKK IAYF+L KTD DMRLMQGDE+
Sbjct: 189 QNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEI 248
Query: 397 KLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDFIWKSTSFDR 456
LRY D + W G+GHVIK+PDN+GDE+ +EL+SS GAP E T F VDF+WKSTSFDR
Sbjct: 249 CLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDR 308
Query: 457 MQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHA 516
MQ AL+ FAVD+ SVS YIYH+LLGH V++V+ +C LPK F+A LPDLN SQVYAVK
Sbjct: 309 MQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTV 368
Query: 517 IQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVV 576
+QRPLSLIQGPPGTGKTVTSATIVY L +Q PVLVCAPSNIAVDQLTEKIH+TGLKVV
Sbjct: 369 LQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVV 428
Query: 577 RVCAKSREAIDSPVSFLALHNQIRNMEMNSXXXXXXXXXXXXXXXSSADEKRYRMLKKNA 636
R+CAKSREAIDSPVSFLALHNQIRNM+ SSADEKRYR LK+ A
Sbjct: 429 RLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTA 488
Query: 637 EKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQLILVGD 696
E+ LL NADVICCTCVGAGDPRL K++F SILIDES QATEPECMVPV+LGAKQLILVGD
Sbjct: 489 ERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGD 548
Query: 697 HCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPSNFFYEGSLQ 756
HCQLGPVVMCKKAA+AGLSQSLFERLVVLGIRP RL+VQYRMHP LS FPSN FYEGSLQ
Sbjct: 549 HCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQ 608
Query: 757 NGVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNVEKITTRFIR 816
NGV A +R DF WP PDKPM FYVTQGQEEIA SGTSY+NRTEA+NVEKITT+ ++
Sbjct: 609 NGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLK 668
Query: 817 CGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMSCV 876
G KP+QIG+ITPYEGQR++LVQ+MQ+ GSL K+YQE+E+ASVDAFQGREKD II+SCV
Sbjct: 669 AGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCV 728
Query: 877 RSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKVLVEGP 936
R+N+HQGIGFLNDPRRLNVALTRA+YG+I++GNPK LSKQPLWN+LLN+YKEQKVLVEGP
Sbjct: 729 RANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGP 788
Query: 937 LNNLKESLILFS 948
LNNL+ESL+ FS
Sbjct: 789 LNNLRESLMQFS 800
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 1011 bits (2613), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 472/617 (76%), Positives = 532/617 (86%)
Query: 332 DGYQYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDMRLM 391
D YQYQNIFGPLVKLEADYDK+LKESQTQ+N+TVRWD+GLNKK IAYF+L KTD DMRLM
Sbjct: 7 DAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLM 66
Query: 392 QGDELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDFIWKS 451
QGDE+ LRY D + W G+GHVIK+PDN+GDE+ +EL+SS GAP E T F VDF+WKS
Sbjct: 67 QGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKS 126
Query: 452 TSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVY 511
TSFDRMQ AL+ FAVD+ SVS YIYH+LLGH V++V+ +C LPK F+A LPDLN SQVY
Sbjct: 127 TSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVY 186
Query: 512 AVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRT 571
AVK +QRPLSLIQGPPGTGKTVTSATIVY L +Q PVLVCAPSNIAVDQLTEKIH+T
Sbjct: 187 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQT 246
Query: 572 GLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSXXXXXXXXXXXXXXXSSADEKRYRM 631
GLKVVR+CAKSREAIDSPVSFLALHNQIRNM+ SSADEKRYR
Sbjct: 247 GLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRA 306
Query: 632 LKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQL 691
LK+ AE+ LL NADVICCTCVGAGDPRL K++F SILIDES QATEPECMVPV+LGAKQL
Sbjct: 307 LKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQL 366
Query: 692 ILVGDHCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPSNFFY 751
ILVGDHCQLGPVVMCKKAA+AGLSQSLFERLVVLGIRP RL+VQYRMHP LS FPSN FY
Sbjct: 367 ILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFY 426
Query: 752 EGSLQNGVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNVEKIT 811
EGSLQNGV A +R DF WP PDKPM FYVTQGQEEIA SGTSY+NRTEA+NVEKIT
Sbjct: 427 EGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKIT 486
Query: 812 TRFIRCGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLI 871
T+ ++ G KP+QIG+ITPYEGQR++LVQ+MQ+ GSL K+YQE+E+ASVDAFQGREKD I
Sbjct: 487 TKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFI 546
Query: 872 IMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKV 931
I+SCVR+N+HQGIGFLNDPRRLNVALTRA+YG+I++GNPK LSKQPLWN+LLN+YKEQKV
Sbjct: 547 ILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKV 606
Query: 932 LVEGPLNNLKESLILFS 948
LVEGPLNNL+ESL+ FS
Sbjct: 607 LVEGPLNNLRESLMQFS 623
>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 = 1010 bits (2612), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 472/617 (76%), Positives = 532/617 (86%)
Query: 332 DGYQYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDMRLM 391
D YQYQNIFGPLVKLEADYDK+LKESQTQ+N+TVRWD+GLNKK IAYF+L KTD DMRLM
Sbjct: 8 DAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLM 67
Query: 392 QGDELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDFIWKS 451
QGDE+ LRY D + W G+GHVIK+PDN+GDE+ +EL+SS GAP E T F VDF+WKS
Sbjct: 68 QGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKS 127
Query: 452 TSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVY 511
TSFDRMQ AL+ FAVD+ SVS YIYH+LLGH V++V+ +C LPK F+A LPDLN SQVY
Sbjct: 128 TSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVY 187
Query: 512 AVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRT 571
AVK +QRPLSLIQGPPGTGKTVTSATIVY L +Q PVLVCAPSNIAVDQLTEKIH+T
Sbjct: 188 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQT 247
Query: 572 GLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSXXXXXXXXXXXXXXXSSADEKRYRM 631
GLKVVR+CAKSREAIDSPVSFLALHNQIRNM+ SSADEKRYR
Sbjct: 248 GLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRA 307
Query: 632 LKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQL 691
LK+ AE+ LL NADVICCTCVGAGDPRL K++F SILIDES QATEPECMVPV+LGAKQL
Sbjct: 308 LKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQL 367
Query: 692 ILVGDHCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPSNFFY 751
ILVGDHCQLGPVVMCKKAA+AGLSQSLFERLVVLGIRP RL+VQYRMHP LS FPSN FY
Sbjct: 368 ILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFY 427
Query: 752 EGSLQNGVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNVEKIT 811
EGSLQNGV A +R DF WP PDKPM FYVTQGQEEIA SGTSY+NRTEA+NVEKIT
Sbjct: 428 EGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKIT 487
Query: 812 TRFIRCGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLI 871
T+ ++ G KP+QIG+ITPYEGQR++LVQ+MQ+ GSL K+YQE+E+ASVDAFQGREKD I
Sbjct: 488 TKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFI 547
Query: 872 IMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKV 931
I+SCVR+N+HQGIGFLNDPRRLNVALTRA+YG+I++GNPK LSKQPLWN+LLN+YKEQKV
Sbjct: 548 ILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKV 607
Query: 932 LVEGPLNNLKESLILFS 948
LVEGPLNNL+ESL+ FS
Sbjct: 608 LVEGPLNNLRESLMQFS 624
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 889 bits (2298), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 437/844 (51%), Positives = 571/844 (67%), Gaps = 62/844 (7%)
Query: 100 HACKYCGIHDPAYVIMCNICKKWFCNGRGHTSGSHIINHLVRAKHKEVTLHKDGPLGETV 159
++C YCGI VI CN CKKWFCN + TS SHI+NHLV + H V+LH D LG+TV
Sbjct: 12 NSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSLHPDSDLGDTV 71
Query: 160 LECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQNSLKDMNWDQEQWKPLIADRSFLS 219
LECY CG +N+F+LGF+ AK+++VVVLLCR PCA K+ NWD +QW+PLI DR LS
Sbjct: 72 LECYNCGRKNVFLLGFVSAKSEAVVVLLCRIPCA---QTKNANWDTDQWQPLIEDRQLLS 128
Query: 220 WLVKVPTEQEQQRGRQVTSAQIAKLEEVWKDNAEATFQDLEKPGVDEDPHQVLLRYEDGY 279
W+ + PTE+E+ + R +T +QI+KLE W+ N +AT D++ P E +LLR
Sbjct: 129 WVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDATINDIDAPEEQEAIPPLLLR----- 183
Query: 280 QYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDGYQYQNI 339
YQ D Y+YQ
Sbjct: 184 -YQ-------------------------------------------------DAYEYQRS 193
Query: 340 FGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDG-DMRLMQGDELKL 398
+GPL+KLEADYDK+LKESQ E+++V W + LN + +A F+L+ + ++++ GDE+ L
Sbjct: 194 YGPLIKLEADYDKQLKESQALEHISVSWSLALNNRHLASFTLSTFESNELKVAIGDEMIL 253
Query: 399 RYSYDASKTWSGLGHVIKIPDNFGDEVGLELK-SSAGAPTEATTGFSVDFIWKSTSFDRM 457
YS W G G+++++P++F D LELK S PT TTGF+ +FIWK TS+DRM
Sbjct: 254 WYSGMQHPDWEGRGYIVRLPNSFQDTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRM 313
Query: 458 QLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAI 517
Q AL+KFA+D +S+S Y+Y+++LGH V ++ F LPK FS PN LN SQ AV H +
Sbjct: 314 QDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNSSQSNAVSHVL 373
Query: 518 QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVR 577
QRPLSLIQGPPGTGKTVTSATIVY L K +LVCAPSN+AVD L K+ GLKVVR
Sbjct: 374 QRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVR 433
Query: 578 VCAKSREAIDSPVSFLALHNQIRNMEMNSXXXXXXXXXXXXXXXSSADEKRYRMLKKNAE 637
+ AKSRE ++S VS LALHN + S++D KR+ L + E
Sbjct: 434 LTAKSREDVESSVSNLALHNLV-GRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTE 492
Query: 638 KSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQLILVGDH 697
+L+ ADV+CCTCVGAGD RL KF ++LIDES QA+EPEC++P++ GAKQ+ILVGDH
Sbjct: 493 AEILNKADVVCCTCVGAGDKRL-DTKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDH 551
Query: 698 CQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPSNFFYEGSLQN 757
QLGPV++ +KAA AGL QSLFERL+ LG P RLEVQYRM+P LS+FPSN FYEGSLQN
Sbjct: 552 QQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQN 611
Query: 758 GVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNVEKITTRFIRC 817
GV ++R + FPWP+ PM+F+ G+EEI+ +GTS++NR EA N E+I T+ R
Sbjct: 612 GVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRD 671
Query: 818 GMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMSCVR 877
G+KPEQIGVITPYEGQRA+++Q+MQ GSL +Y ++EVASVDAFQGREKD II+SCVR
Sbjct: 672 GVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVR 731
Query: 878 SNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKVLVEGPL 937
+N+ Q IGFL DPRRLNV LTRAKYG++++GNP+ L++ LWN+LL ++E+ LVEG L
Sbjct: 732 ANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTL 791
Query: 938 NNLK 941
+NL+
Sbjct: 792 DNLQ 795
>pdb|2IYK|A Chain A, Crystal Structure Of The Upf2-Interacting Domain Of
Nonsense Mediated Mrna Decay Factor Upf1
pdb|2IYK|B Chain B, Crystal Structure Of The Upf2-Interacting Domain Of
Nonsense Mediated Mrna Decay Factor Upf1
Length = 162
Score = 275 bits (703), Expect = 9e-74, Method: Compositional matrix adjust.
Identities = 122/155 (78%), Positives = 137/155 (88%)
Query: 97 LPPHACKYCGIHDPAYVIMCNICKKWFCNGRGHTSGSHIINHLVRAKHKEVTLHKDGPLG 156
LP HAC YCGIHDPA V+ CN KKWFCNGRG+TSGSHI+NHLVRAK KEVTLHKDGPLG
Sbjct: 8 LPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLG 67
Query: 157 ETVLECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQNSLKDMNWDQEQWKPLIADRS 216
ETVLECY CG RN+F+LGFIPAKADSVVVLLCR PCA+Q+SLKD+NWD QW+PLI DR
Sbjct: 68 ETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRC 127
Query: 217 FLSWLVKVPTEQEQQRGRQVTSAQIAKLEEVWKDN 251
FLSWLVK+P+EQEQ R RQ+T+ QI KLEE+WK+N
Sbjct: 128 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 162
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 189 bits (481), Expect = 4e-48, Method: Compositional matrix adjust.
Identities = 149/457 (32%), Positives = 225/457 (49%), Gaps = 47/457 (10%)
Query: 505 LNRSQVYAVKHAI-QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQ 563
L+ SQ AV A+ Q+ L++I GPPGTGKT T I+ Q VKQ G VL CAPSNIAVD
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ-GLKVLCCAPSNIAVDN 248
Query: 564 LTEKIHRTGLKVVRVCAKSR-------EAIDSPVSFLALHNQIRNMEMNSXXXXXXXXXX 616
L E++ +++R+ +R ++D+ ++ + ++ +
Sbjct: 249 LVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKT 308
Query: 617 XXXXXSSADEKRYRMLKKN----AEKSLLD---NADVICCTCVGAGDPRLLKI----KFH 665
S ++L+K E ++L+ +A+V+ T GA LK+ F
Sbjct: 309 QDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFD 368
Query: 666 SILIDESMQATEPECMVPVILGAKQLILVGDHCQLGPVVMCKKAARAGLSQSLFERLV-V 724
++IDE QA E C +P +L A++ IL GDH QL P + KAA AGLS SL ERL
Sbjct: 369 VVVIDECAQALEASCWIP-LLKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEE 427
Query: 725 LGIRPFR-LEVQYRMHPELSKFPSNFFYEGSLQNGVCADERKLSKIDFPWPVPDK----P 779
G R R L VQYRMH + ++ S+ Y G L + R L + D P + P
Sbjct: 428 YGARVVRTLTVQYRMHQAIMRWASDTMYLGQL-TAHSSVARHLLR-DLPGVAATEETGVP 485
Query: 780 MLFYVTQG-------QEEIAGSGTSYVNRTEASNVEKITTRFIRCGMKPEQIGVITPYEG 832
+L T G +E+ G N E V + G+ I V++PY
Sbjct: 486 LLLVDTAGCGLFELEEEDEQSKG----NPGEVRLVSLHIQALVDAGVPARDIAVVSPYNL 541
Query: 833 QRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMSCVRSNDHQGIGFLNDPRR 892
Q L Q + ++ + E+E+ SVD FQGREK+ +I+S VRSN +GFL + RR
Sbjct: 542 QVDLLRQSLVHR-------HPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRR 594
Query: 893 LNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQ 929
+NVA+TRA+ + VI + + ++ L+ ++ +
Sbjct: 595 INVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQH 631
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 189 bits (481), Expect = 4e-48, Method: Compositional matrix adjust.
Identities = 148/457 (32%), Positives = 222/457 (48%), Gaps = 47/457 (10%)
Query: 505 LNRSQVYAVKHAI-QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQ 563
L+ SQ AV A+ Q+ L++I GPPGTGKT T I+ Q VKQ G VL CAPSNIAVD
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ-GLKVLCCAPSNIAVDN 248
Query: 564 LTEKIHRTGLKVVRVCAKSR-------EAIDSPVSFLALHNQIRNMEMNSXXXXXXXXXX 616
L E++ +++R+ +R ++D+ ++ + ++ +
Sbjct: 249 LVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKT 308
Query: 617 XXXXXSSADEKRYRMLKKN----AEKSLLD---NADVICCTCVGAGDPRLLKI----KFH 665
S ++L+K E ++L+ +A+V+ T GA LK+ F
Sbjct: 309 QDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFD 368
Query: 666 SILIDESMQATEPECMVPVILGAKQLILVGDHCQLGPVVMCKKAARAGLSQSLFERLV-V 724
++IDE QA E C +P +L A++ IL GDH QL P + KAA AGLS SL ERL
Sbjct: 369 VVVIDECAQALEASCWIP-LLKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEE 427
Query: 725 LGIRPFR-LEVQYRMHPELSKFPSNFFYEGSLQNGVCADERKLSKIDFPWPVPDK----P 779
G R R L VQYRMH + ++ S+ Y G L L D P + P
Sbjct: 428 YGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLR--DLPGVAATEETGVP 485
Query: 780 MLFYVTQG-------QEEIAGSGTSYVNRTEASNVEKITTRFIRCGMKPEQIGVITPYEG 832
+L T G +E+ G N E V + G+ I V++PY
Sbjct: 486 LLLVDTAGCGLFELEEEDEQSKG----NPGEVRLVSLHIQALVDAGVPARDIAVVSPYNL 541
Query: 833 QRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMSCVRSNDHQGIGFLNDPRR 892
Q L Q + ++ + E+E+ SVD FQGREK+ +I+S VRSN +GFL + RR
Sbjct: 542 QVDLLRQSLVHR-------HPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRR 594
Query: 893 LNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQ 929
+NVA+TRA+ + VI + + ++ L+ ++ +
Sbjct: 595 INVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQH 631
>pdb|3E1S|A Chain A, Structure Of An N-Terminal Truncation Of Deinococcus
Radiodurans Recd2
pdb|3GP8|A Chain A, Crystal Structure Of The Binary Complex Of Recd2 With Dna
pdb|3GPL|A Chain A, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
pdb|3GPL|B Chain B, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
Length = 574
Score = 36.6 bits (83), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCA 580
L ++ G PGTGK+ T+ + L + G V +CAP+ A +L E RT V R+
Sbjct: 206 LVVLTGGPGTGKSTTTKAVA-DLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLG 264
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 35.0 bits (79), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLT 565
G GTGKTVT A ++ L G P LV AP+ I QL
Sbjct: 36 GATGTGKTVTMAKVIEAL----GRPALVLAPNKILAAQLA 71
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 35.0 bits (79), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLT 565
G GTGKTVT A ++ L G P LV AP+ I QL
Sbjct: 35 GATGTGKTVTMAKVIEAL----GRPALVLAPNKILAAQLA 70
>pdb|3DMD|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3DMD|A Chain A, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3DMD|C Chain C, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3E70|C Chain C, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVR 577
G G+GKT T A + L K G V++ A A++QL E R G+KV++
Sbjct: 136 GFNGSGKTTTIAKLANWL-KNHGFSVVIAASDTFRAGAIEQLEEHAKRIGVKVIK 189
>pdb|3DM9|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 31.2 bits (69), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVR 577
G G+GKT T A + L K G V++ A A++QL E R G+KV++
Sbjct: 136 GFNGSGKTTTIAKLANWL-KNHGFSVVIAASDTFRAGAIEQLEEHAKRIGVKVIK 189
>pdb|2JC3|A Chain A, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
pdb|2JC3|B Chain B, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
pdb|2JC3|C Chain C, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
pdb|2JC3|D Chain D, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
pdb|2JC3|E Chain E, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
pdb|2JC3|F Chain F, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
pdb|2JC3|G Chain G, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
pdb|2JC3|H Chain H, Structure Of O-acetylserine Sulfhydrylase B From
Salmonella Typhimurium
Length = 303
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 3/84 (3%)
Query: 752 EGSLQNGVCADERKLSKIDFPWPVPDKPMLFYVTQGQE---EIAGSGTSYVNRTEASNVE 808
EG+ + ER K+ + PD P Y T G E + +G T +V+ +
Sbjct: 120 EGARDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTI 179
Query: 809 KITTRFIRCGMKPEQIGVITPYEG 832
+RF+R KP I + P EG
Sbjct: 180 TGVSRFLREQEKPVTIVGLQPEEG 203
>pdb|1WYD|A Chain A, Crystal Structure Of Aspartyl-Trna Synthetase From
Sulfolobus Tokodaii
pdb|1WYD|B Chain B, Crystal Structure Of Aspartyl-Trna Synthetase From
Sulfolobus Tokodaii
Length = 429
Score = 30.8 bits (68), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 686 LGAKQLILVGDHCQLGPVVMCKKAARAGLSQSLFERLVV 724
LG K+ I++ D LG VV+ K ++ G+SQ L + V+
Sbjct: 31 LGGKKFIILRDKTGLGQVVVDKNSSAFGISQELTQESVI 69
>pdb|4F33|B Chain B, Crystal Structure Of Therapeutic Antibody Morab-009
pdb|4F33|D Chain D, Crystal Structure Of Therapeutic Antibody Morab-009
pdb|4F33|F Chain F, Crystal Structure Of Therapeutic Antibody Morab-009
pdb|4F33|H Chain H, Crystal Structure Of Therapeutic Antibody Morab-009
pdb|4F3F|B Chain B, Crystal Structure Of Msln7-64 Morab-009 Fab Complex
Length = 231
Score = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 818 GMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMSCVR 877
G E IG+ITPY G ++ + +++G + + A +D +D + C R
Sbjct: 42 GKSLEWIGLITPYNGASSY---NQKFRGKATLTVDKSSSTAYMDLLSLTSEDSAVYFCAR 98
Query: 878 SNDHQGIGF 886
+ G GF
Sbjct: 99 -GGYDGRGF 106
>pdb|3C5Z|A Chain A, Crystal Structure Of Mouse Mhc Class Ii I-Ab3K PEPTIDE
COMPLEXED WITH Mouse Tcr B3k506
pdb|3C5Z|E Chain E, Crystal Structure Of Mouse Mhc Class Ii I-Ab3K PEPTIDE
COMPLEXED WITH Mouse Tcr B3k506
Length = 202
Score = 30.0 bits (66), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 30/110 (27%), Positives = 54/110 (49%), Gaps = 10/110 (9%)
Query: 380 SLAKTDGDMRLMQGDELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAPTEA 439
S+ +T+G++ L + D L + +Y AS + L ++ P G+ ++S +
Sbjct: 2 SVTQTEGNVALSEEDFLTIHCNYSASG-YPALFWYVQYP---GEGPQFLFRASRDKEKGS 57
Query: 440 TTGFSVDFIWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLF 489
+ GF + +TSF LRK +V +S SA Y L+ N ++V+F
Sbjct: 58 SRGFEATYDKGTTSF-----HLRKASV-QESDSAVYYCALVISNTNKVVF 101
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 0.135 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,388,270
Number of Sequences: 62578
Number of extensions: 1133155
Number of successful extensions: 2963
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2926
Number of HSP's gapped (non-prelim): 26
length of query: 959
length of database: 14,973,337
effective HSP length: 108
effective length of query: 851
effective length of database: 8,214,913
effective search space: 6990890963
effective search space used: 6990890963
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)