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= 002070
(973 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 256 bits (653), Expect = 6e-68, Method: Compositional matrix adjust.
Identities = 229/751 (30%), Positives = 341/751 (45%), Gaps = 136/751 (18%)
Query: 160 FAPHWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQNRAVEGD 219
F ++S V L+ G ++ +++ +N LE + VLI G NRA GD
Sbjct: 231 FPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGD 290
Query: 220 FVLIKVDRLSLWAKMKGFSNNSSIVEDSNLPTEANGMHSDICKGKSKVDVSYEYSNCTLL 279
V++++ S W SSIV DS H D+ D+
Sbjct: 291 QVIVELLPQSEWKA------PSSIVLDSE--------HFDV---NDNPDI---------- 323
Query: 280 SEKGIHHDDDSSSEAYNQEMIEREGYNYINGHHPXXXXXXXXXXXXQQNDGMNAIERLSA 339
E G DDD++ + N +I +D + A
Sbjct: 324 -EAG--DDDDNNESSSNTTVI---------------------------SDKQRRLLAKDA 353
Query: 340 MISSYPTK-RPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDR 398
MI+ K +PT +VV I RS W Y G + +SS +
Sbjct: 354 MIAQRSKKIQPTAKVVYIQRRS--------------WRQYVGQLAPSSVDPQSSST---- 395
Query: 399 EYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHV 458
+ ++++ K LP ++ R ++ +V + ID W +P H
Sbjct: 396 ----------QNVFVILMDKCLP-KVRIRTRRAAELLDKRIVIS-IDSWPTTHKYPLGHF 443
Query: 459 LHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCV------------PWEVPQEEL 506
+ G + + A+L E+ + FS + L CLP P V ++ L
Sbjct: 444 VRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPL 503
Query: 507 LS-RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEA 565
L+ RKDLR+ I +IDP D++DAL ++L +G VGVHIADV++FV PGTALD E
Sbjct: 504 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEG 563
Query: 566 QVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIR 625
R TSVY++ ++I MLP+LL ++ SL P VDR AFS+ W+L+ + ++V+ ++VIR
Sbjct: 564 AARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIR 623
Query: 626 SCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKR 685
S SYE AQ ID K ++ L G +++L ++S LK KR
Sbjct: 624 SREAFSYEQAQLRIDDK---TQNDELTMG----------------MRALLKLSVKLKQKR 664
Query: 686 FTDGALRLENSK-PVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPD 744
GAL L + + V + E P + + N L EEFMLLAN + A I AFP
Sbjct: 665 LEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQ 724
Query: 745 SALLRRHPAP---NMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDI 801
+A+LRRH AP N L E ++ + + SS SL++ + +D Y F+
Sbjct: 725 TAMLRRHAAPPSTNFEILNEM--LNTRKNMSISLESSKALADSLDRCVDP-EDPY--FNT 779
Query: 802 LIN-YATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAAL 860
L+ +TR M A YF SG + D+ HY LA +YTHFTSP+RRY D+V HR L A+
Sbjct: 780 LVRIMSTRCMMAAQYFYSGAYS-YPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAI 838
Query: 861 EAEKLYWKHR-----RMLPKNNHREGVRGRF 886
E L HR M+ +N +R+ +F
Sbjct: 839 GYEPLSLTHRDKNKMDMICRNINRKHRNAQF 869
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 255 bits (652), Expect = 7e-68, Method: Compositional matrix adjust.
Identities = 230/751 (30%), Positives = 340/751 (45%), Gaps = 136/751 (18%)
Query: 160 FAPHWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQNRAVEGD 219
F ++S V L+ G ++ +++ +N LE + VLI G NRA GD
Sbjct: 257 FPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGD 316
Query: 220 FVLIKVDRLSLWAKMKGFSNNSSIVEDSNLPTEANGMHSDICKGKSKVDVSYEYSNCTLL 279
V++++ S W SSIV DS H D+ D+
Sbjct: 317 QVIVELLPQSEWKA------PSSIVLDSE--------HFDV---NDNPDI---------- 349
Query: 280 SEKGIHHDDDSSSEAYNQEMIEREGYNYINGHHPXXXXXXXXXXXXQQNDGMNAIERLSA 339
E G DDD++ + N +I +D + A
Sbjct: 350 -EAG--DDDDNNESSSNTTVI---------------------------SDKQRRLLAKDA 379
Query: 340 MISSYPTK-RPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDR 398
MI+ K +PT +VV I RS W Y G P
Sbjct: 380 MIAQRSKKIQPTAKVVYIQRRS--------------WRQYVGQL------------APSS 413
Query: 399 EYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHV 458
Q + T + ++++ K LP ++ R ++ +V + ID W +P H
Sbjct: 414 VDPQSSSTQNVF--VILMDKCLP-KVRIRTRRAAELLDKRIVIS-IDSWPTTHKYPLGHF 469
Query: 459 LHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCV------------PWEVPQEEL 506
+ G + + A+L E+ + FS + L CLP P V ++ L
Sbjct: 470 VRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPL 529
Query: 507 LS-RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEA 565
L+ RKDLR+ I +IDP D++DAL ++L +G VGVHIADV++FV PGTALD E
Sbjct: 530 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEG 589
Query: 566 QVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIR 625
R TSVY++ ++I MLP+LL ++ SL P VDR AFS+ W+L+ + ++V+ ++VIR
Sbjct: 590 AARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIR 649
Query: 626 SCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKR 685
S SYE AQ ID K ++ L G +++L ++S LK KR
Sbjct: 650 SREAFSYEQAQLRIDDK---TQNDELTMG----------------MRALLKLSVKLKQKR 690
Query: 686 FTDGALRLENSK-PVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPD 744
GAL L + + V + E P + + N L EEFMLLAN + A I AFP
Sbjct: 691 LEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQ 750
Query: 745 SALLRRHPAP---NMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDI 801
+A+LRRH AP N L E ++ + + SS SL++ + +D Y F+
Sbjct: 751 TAMLRRHAAPPSTNFEILNEM--LNTRKNMSISLESSKALADSLDRCVDP-EDPY--FNT 805
Query: 802 LIN-YATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAAL 860
L+ +TR M A YF SG + D+ HY LA +YTHFTSP+RRY D+V HR L A+
Sbjct: 806 LVRIMSTRCMMAAQYFYSGAYS-YPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAI 864
Query: 861 EAEKLYWKHR-----RMLPKNNHREGVRGRF 886
E L HR M+ +N +R+ +F
Sbjct: 865 GYEPLSLTHRDKNKMDMICRNINRKHRNAQF 895
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
Length = 760
Score = 234 bits (597), Expect = 2e-61, Method: Compositional matrix adjust.
Identities = 162/447 (36%), Positives = 226/447 (50%), Gaps = 39/447 (8%)
Query: 440 VAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCV-- 497
+ ID W +P H + G + + A+L E+ + FS + L CLP
Sbjct: 208 IVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGH 267
Query: 498 ----------PWEVPQEELLS-RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGV 546
P V ++ LL+ RKDLR+ I +IDP D++DAL ++L +G VGV
Sbjct: 268 DWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGV 327
Query: 547 HIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFW 606
HIADV++FV PGTALD E R TSVY++ ++I LP LL ++ SL P VDR AFS+ W
Sbjct: 328 HIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDXLPXLLGTDLCSLKPYVDRFAFSVIW 387
Query: 607 DLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSD 666
+L+ + ++V+ ++VIRS SYE AQ ID K ++ L G
Sbjct: 388 ELDDSANIVNVNFXKSVIRSREAFSYEQAQLRIDDK---TQNDELTXG------------ 432
Query: 667 VVRSIKSLYEVSKILKDKRFTDGALRLENSK-PVFLFDEYGTPYDSVLSGREDLNFLFEE 725
++L ++S LK KR GAL L + + V E P + + N L EE
Sbjct: 433 ----XRALLKLSVKLKQKRLEAGALNLASPEVKVHXDSETSDPNEVEIKKLLATNSLVEE 488
Query: 726 FMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREF-EAFCSKHGLQLDTSSSGQFHQS 784
F LLAN + A I AFP +A LRRH AP E ++ + SS S
Sbjct: 489 FXLLANISVARKIYDAFPQTAXLRRHAAPPSTNFEILNEXLNTRKNXSISLESSKALADS 548
Query: 785 LEQAREKLKDDYVLFDILINY-ATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSP 843
L++ + +D Y F+ L+ +TR A YF SG + D+ HY LA +YTHFTSP
Sbjct: 549 LDRCVDP-EDPY--FNTLVRIXSTRCXXAAQYFYSGAYS-YPDFRHYGLAVDIYTHFTSP 604
Query: 844 LRRYPDLVVHRTLNAALEAEKLYWKHR 870
+RRY D+V HR L A+ E L HR
Sbjct: 605 IRRYCDVVAHRQLAGAIGYEPLSLTHR 631
Score = 35.4 bits (80), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 36/123 (29%), Positives = 56/123 (45%), Gaps = 9/123 (7%)
Query: 160 FAPHWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQNRAVEGD 219
F ++S V L+ G ++ +++ +N LE + VLI G NRA GD
Sbjct: 14 FPEYYSTARVXGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGD 73
Query: 220 FVLIKVDRLSLWAKMKGFSNNSSIVEDSNLPTEANGMHSDICKGKSKVDVSYEYSNCTLL 279
V++++ S W SSIV DS + N + DI G D + SN T++
Sbjct: 74 QVIVELLPQSEWKAP------SSIVLDSE-HFDVND-NPDIEAGDDD-DNNESSSNTTVI 124
Query: 280 SEK 282
S+K
Sbjct: 125 SDK 127
>pdb|2IX0|A Chain A, Rnase Ii
Length = 663
Score = 87.0 bits (214), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 93/362 (25%), Positives = 150/362 (41%), Gaps = 29/362 (8%)
Query: 504 EELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDI 563
+E L R+DL TID ++ D+DDAL + L D ++ V IAD + ++ G+ LD
Sbjct: 203 DEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 262
Query: 564 EAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRW-IGRT 622
A++R+ + Y+ IPMLP LS+++ SL R + L++ G + D
Sbjct: 263 AAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAA 322
Query: 623 VIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILK 682
I S KL Y+ D ++ D W Q E + ++ L ++ +
Sbjct: 323 TIESKAKLVYDQVSDWLENTGD----------W-----QPESEAIAEQVRLLAQICQRRG 367
Query: 683 DKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAF 742
+ R + + F+ E G D V R N + EE M+ AN AA V+ R
Sbjct: 368 EWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVL-RDK 426
Query: 743 PDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDIL 802
+ H + A HGL +D + RE D
Sbjct: 427 LGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLD-- 484
Query: 803 INYATRPMQLASYFCSGDFKDDTDWG-HYALAFPVYTHFTSPLRRYPDLVVHRTLNAALE 861
+R + S+ + T+ G H+ L Y +TSP+R+Y D++ HR L A ++
Sbjct: 485 ----SRIRRFQSF-----AEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIK 535
Query: 862 AE 863
E
Sbjct: 536 GE 537
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
Length = 664
Score = 85.1 bits (209), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 92/362 (25%), Positives = 150/362 (41%), Gaps = 29/362 (8%)
Query: 504 EELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDI 563
+E L R+DL TID ++ D++DAL + L D ++ V IAD + ++ G+ LD
Sbjct: 204 DEGLVREDLTALDFVTIDSASTEDMNDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 263
Query: 564 EAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRW-IGRT 622
A++R+ + Y+ IPMLP LS+++ SL R + L++ G + D
Sbjct: 264 AAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAA 323
Query: 623 VIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILK 682
I S KL Y+ D ++ D W Q E + ++ L ++ +
Sbjct: 324 TIESKAKLVYDQVSDWLENTGD----------W-----QPESEAIAEQVRLLAQICQRRG 368
Query: 683 DKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAF 742
+ R + + F+ E G D V R N + EE M+ AN AA V+ R
Sbjct: 369 EWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVL-RDK 427
Query: 743 PDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDIL 802
+ H + A HGL +D + RE D
Sbjct: 428 LGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLD-- 485
Query: 803 INYATRPMQLASYFCSGDFKDDTDWG-HYALAFPVYTHFTSPLRRYPDLVVHRTLNAALE 861
+R + S+ + T+ G H+ L Y +TSP+R+Y D++ HR L A ++
Sbjct: 486 ----SRIRRFQSF-----AEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIK 536
Query: 862 AE 863
E
Sbjct: 537 GE 538
>pdb|2R7D|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|B Chain B, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|C Chain C, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7F|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Hexagonal Crystal Form.
Northeast Structural Genomics Target Drr63
Length = 469
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 50/141 (35%), Positives = 75/141 (53%), Gaps = 17/141 (12%)
Query: 502 PQEELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTAL 561
P EE R DL + F ID D DDA+ +E L G++R+ VH+ADV+ V P + L
Sbjct: 77 PAEE---RLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPL 133
Query: 562 DIEAQVRSTSVYMLQRKIPMLPVLLSEEVG----SLNPGVDRLAFSIFWDLNSAG--DVV 615
D+EA+ R ++Y+ R I LP L + G ++P A SI DL+ G + V
Sbjct: 134 DLEARARGATLYLPDRTIGXLPDELVAKAGLGLHEVSP-----ALSICLDLDPDGNAEAV 188
Query: 616 DRWIGRTVIRSCCKLSYEHAQ 636
D + R ++ +L+Y+ AQ
Sbjct: 189 DVLLTRVKVQ---RLAYQEAQ 206
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 19/32 (59%)
Query: 829 HYALAFPVYTHFTSPLRRYPDLVVHRTLNAAL 860
H+ +Y TSP RRY DLVVH+ L A L
Sbjct: 327 HHGXGLDLYAQATSPXRRYLDLVVHQQLRAFL 358
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii
pdb|2ID0|B Chain B, Escherichia Coli Rnase Ii
pdb|2ID0|C Chain C, Escherichia Coli Rnase Ii
pdb|2ID0|D Chain D, Escherichia Coli Rnase Ii
Length = 644
Score = 70.5 bits (171), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 91/362 (25%), Positives = 146/362 (40%), Gaps = 29/362 (8%)
Query: 504 EELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDI 563
+E L R+DL TID ++ D DDAL + L D ++ V IAD + ++ G+ LD
Sbjct: 184 DEGLVREDLTALDFVTIDSASTEDXDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 243
Query: 564 EAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRW-IGRT 622
A++R+ + Y+ IP LP LS+++ SL R + L++ G + D
Sbjct: 244 AAKIRAFTNYLPGFNIPXLPRELSDDLCSLRANEVRPVLACRXTLSADGTIEDNIEFFAA 303
Query: 623 VIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILK 682
I S KL Y+ D ++ D W Q E + ++ L ++ +
Sbjct: 304 TIESKAKLVYDQVSDWLENTGD----------W-----QPESEAIAEQVRLLAQICQRRG 348
Query: 683 DKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAF 742
+ R + + F+ E G D V R N + EE + AN AA V+ R
Sbjct: 349 EWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAXIAANICAARVL-RDK 407
Query: 743 PDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDIL 802
+ H + A HGL +D + RE D
Sbjct: 408 LGFGIYNVHXGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLD-- 465
Query: 803 INYATRPMQLASYFCSGDFKDDTDWG-HYALAFPVYTHFTSPLRRYPDLVVHRTLNAALE 861
+R + S+ + T+ G H+ L Y +TSP+R+Y D + HR L A ++
Sbjct: 466 ----SRIRRFQSF-----AEISTEPGPHFGLGLEAYATWTSPIRKYGDXINHRLLKAVIK 516
Query: 862 AE 863
E
Sbjct: 517 GE 518
>pdb|1BPO|A Chain A, Clathrin Heavy-Chain Terminal Domain And Linker
pdb|1BPO|B Chain B, Clathrin Heavy-Chain Terminal Domain And Linker
pdb|1BPO|C Chain C, Clathrin Heavy-Chain Terminal Domain And Linker
Length = 494
Score = 34.3 bits (77), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 163 HWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTD-----VLITGIAAQNRAVE 217
HWSME ++ ++ D +L A C+I +TD +L+TGI+AQ V
Sbjct: 129 HWSMEGESQPVKMFDRHSSL----------AGCQIINYRTDAKQKWLLLTGISAQQNRVV 178
Query: 218 GDFVLIKVDR 227
G L VDR
Sbjct: 179 GAMQLYSVDR 188
>pdb|1XI4|A Chain A, Clathrin D6 Coat
pdb|1XI4|B Chain B, Clathrin D6 Coat
pdb|1XI4|C Chain C, Clathrin D6 Coat
pdb|1XI4|D Chain D, Clathrin D6 Coat
pdb|1XI4|E Chain E, Clathrin D6 Coat
pdb|1XI4|F Chain F, Clathrin D6 Coat
pdb|1XI4|G Chain G, Clathrin D6 Coat
pdb|1XI4|H Chain H, Clathrin D6 Coat
pdb|1XI4|I Chain I, Clathrin D6 Coat
pdb|1XI5|A Chain A, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|B Chain B, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|C Chain C, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|D Chain D, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|E Chain E, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|F Chain F, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|G Chain G, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|H Chain H, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|I Chain I, Clathrin D6 Coat With Auxilin J-Domain
pdb|3IYV|A Chain A, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|B Chain B, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|C Chain C, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|D Chain D, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|E Chain E, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|F Chain F, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|G Chain G, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|H Chain H, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|I Chain I, Clathrin D6 Coat As Full-Length Triskelions
Length = 1630
Score = 34.3 bits (77), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 163 HWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTD-----VLITGIAAQNRAVE 217
HWSME ++ ++ D +L A C+I +TD +L+TGI+AQ V
Sbjct: 129 HWSMEGESQPVKMFDRHSSL----------AGCQIINYRTDAKQKWLLLTGISAQQNRVV 178
Query: 218 GDFVLIKVDR 227
G L VDR
Sbjct: 179 GAMQLYSVDR 188
>pdb|1C9L|A Chain A, Peptide-In-Groove Interactions Link Target Proteins To The
B-Propeller Of Clathrin
pdb|1C9L|B Chain B, Peptide-In-Groove Interactions Link Target Proteins To The
B-Propeller Of Clathrin
Length = 357
Score = 34.3 bits (77), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 163 HWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTD-----VLITGIAAQNRAVE 217
HWSME ++ ++ D +L A C+I +TD +L+TGI+AQ V
Sbjct: 127 HWSMEGESQPVKMFDRHSSL----------AGCQIINYRTDAKQKWLLLTGISAQQNRVV 176
Query: 218 GDFVLIKVDR 227
G L VDR
Sbjct: 177 GAMQLYSVDR 186
>pdb|4G55|A Chain A, Clathrin Terminal Domain Complexed With Pitstop 2
Length = 369
Score = 34.3 bits (77), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 163 HWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTD-----VLITGIAAQNRAVE 217
HWSME ++ ++ D +L A C+I +TD +L+TGI+AQ V
Sbjct: 134 HWSMEGESQPVKMFDRHSSL----------AGCQIINYRTDAKQKWLLLTGISAQQNRVV 183
Query: 218 GDFVLIKVDR 227
G L VDR
Sbjct: 184 GAMQLYSVDR 193
>pdb|1C9I|A Chain A, Peptide-In-Groove Interactions Link Target Proteins To The
B-Propeller Of Clathrin
pdb|1C9I|B Chain B, Peptide-In-Groove Interactions Link Target Proteins To The
B-Propeller Of Clathrin
Length = 359
Score = 34.3 bits (77), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 163 HWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTD-----VLITGIAAQNRAVE 217
HWSME ++ ++ D +L A C+I +TD +L+TGI+AQ V
Sbjct: 129 HWSMEGESQPVKMFDRHSSL----------AGCQIINYRTDAKQKWLLLTGISAQQNRVV 178
Query: 218 GDFVLIKVDR 227
G L VDR
Sbjct: 179 GAMQLYSVDR 188
>pdb|1UTC|A Chain A, Clathrin Terminal Domain Complexed With Tlpwdlwtt
pdb|1UTC|B Chain B, Clathrin Terminal Domain Complexed With Tlpwdlwtt
pdb|3GC3|B Chain B, Crystal Structure Of Arrestin2s And Clathrin
pdb|3GD1|I Chain I, Structure Of An ArrestinCLATHRIN COMPLEX REVEALS A NOVEL
Clathrin Binding Domain That Modulates Receptor
Trafficking
Length = 363
Score = 34.3 bits (77), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 163 HWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTD-----VLITGIAAQNRAVE 217
HWSME ++ ++ D +L A C+I +TD +L+TGI+AQ V
Sbjct: 129 HWSMEGESQPVKMFDRHSSL----------AGCQIINYRTDAKQKWLLLTGISAQQNRVV 178
Query: 218 GDFVLIKVDR 227
G L VDR
Sbjct: 179 GAMQLYSVDR 188
>pdb|2XZG|A Chain A, Clathrin Terminal Domain Complexed With Pitstop 1
Length = 365
Score = 33.9 bits (76), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 163 HWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTD-----VLITGIAAQNRAVE 217
HWSME ++ ++ D +L A C+I +TD +L+TGI+AQ V
Sbjct: 130 HWSMEGESQPVKMFDRHSSL----------AGCQIINYRTDAKQKWLLLTGISAQQNRVV 179
Query: 218 GDFVLIKVDR 227
G L VDR
Sbjct: 180 GAMQLYSVDR 189
>pdb|3MWE|B Chain B, Truncated Human Atp-Citrate Lyase With Tartrate Bound
Length = 335
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 815 YFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDL 850
Y +GD K WGH + PV+ + +R++P++
Sbjct: 45 YPFTGDHKQKFYWGHKEILIPVFKNMADAMRKHPEV 80
>pdb|3PFF|A Chain A, Truncated Human Atp-Citrate Lyase With Adp And Tartrate
Bound
Length = 829
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 815 YFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVV 852
Y +GD K WGH + PV+ + +R++P++ V
Sbjct: 531 YPFTGDHKQKFYWGHKEILIPVFKNMADAMRKHPEVDV 568
>pdb|1HUX|A Chain A, Crystal Structure Of The Acidaminococcus Fermentans (R)-2-
Hydroxyglutaryl-Coa Dehydratase Component A
pdb|1HUX|B Chain B, Crystal Structure Of The Acidaminococcus Fermentans (R)-2-
Hydroxyglutaryl-Coa Dehydratase Component A
Length = 270
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 157 CKIFAPHWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQNRAV 216
C +FA + +++ +K D ++R + +R+ G+ DV++TG AQN V
Sbjct: 166 CTVFAESEVISQLSKGTDKIDIIAGIHR-SVASRVIGLANRVGIVKDVVMTGGVAQNYGV 224
Query: 217 EG 218
G
Sbjct: 225 RG 226
>pdb|3MWD|B Chain B, Truncated Human Atp-Citrate Lyase With Citrate Bound
Length = 334
Score = 29.6 bits (65), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 25/54 (46%)
Query: 799 FDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVV 852
FD + + + Y +GD K WGH + PV+ + R++P++ V
Sbjct: 29 FDYVCSRDEPSVAAXVYPFTGDHKQKFYWGHKEILIPVFKNXADAXRKHPEVDV 82
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 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,824,574
Number of Sequences: 62578
Number of extensions: 1144636
Number of successful extensions: 2560
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2533
Number of HSP's gapped (non-prelim): 26
length of query: 973
length of database: 14,973,337
effective HSP length: 108
effective length of query: 865
effective length of database: 8,214,913
effective search space: 7105899745
effective search space used: 7105899745
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: 56 (26.2 bits)