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= 008167
(575 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 499 bits (1286), Expect = e-141, Method: Compositional matrix adjust.
Identities = 255/529 (48%), Positives = 348/529 (65%), Gaps = 19/529 (3%)
Query: 7 SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
S S + + D+ +PK+RI+TR+ LLDKRI++++DSW +YP GH+VR +G I
Sbjct: 392 SSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIE 451
Query: 67 DRDTESEMVLIDNDIDARPFSTQVLACLPPL------------PWSVSSEDLANPIRLDL 114
E+E +L+++D++ RPFS +VL CLP P +VS + L R DL
Sbjct: 452 SAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTK-RKDL 510
Query: 115 RDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSV 174
RD + S+DPPGC DI+DALH L +GN+EVGVHIADVT+FV PGT LD E + RGTSV
Sbjct: 511 RDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSV 570
Query: 175 YLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY 234
YLV++RIDMLP L D+CSL+ V+R AFSVIWEL A I++ + KSVI+S A SY
Sbjct: 571 YLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSY 630
Query: 235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 294
+AQ R+DD D LT +R + L+ K++Q+R+E GAL LAS EVK +D+ET DP +
Sbjct: 631 EQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNE 690
Query: 295 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAA 351
+ + ++ N +VEEFML AN+SVA +I FP ++LRRH PS E+L +L T
Sbjct: 691 VEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRK 750
Query: 352 AVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHY 410
+ ++L+ SSKALADSLDR V +DPYFN L+RI++TRCM A YF SG + P+F HY
Sbjct: 751 NMSISLE--SSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHY 808
Query: 411 GLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQ 470
GLA +YTHFTSPIRRY DVV HR L+ ++G L +D+ ++ I N+N +HRNAQ
Sbjct: 809 GLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQ 868
Query: 471 MASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519
A R S+E + R + ++K+ +NG +V VPKFG+EG + L
Sbjct: 869 FAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRL 917
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 499 bits (1285), Expect = e-141, Method: Compositional matrix adjust.
Identities = 255/529 (48%), Positives = 348/529 (65%), Gaps = 19/529 (3%)
Query: 7 SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
S S + + D+ +PK+RI+TR+ LLDKRI++++DSW +YP GH+VR +G I
Sbjct: 418 SSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIE 477
Query: 67 DRDTESEMVLIDNDIDARPFSTQVLACLPPL------------PWSVSSEDLANPIRLDL 114
E+E +L+++D++ RPFS +VL CLP P +VS + L R DL
Sbjct: 478 SAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTK-RKDL 536
Query: 115 RDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSV 174
RD + S+DPPGC DI+DALH L +GN+EVGVHIADVT+FV PGT LD E + RGTSV
Sbjct: 537 RDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSV 596
Query: 175 YLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY 234
YLV++RIDMLP L D+CSL+ V+R AFSVIWEL A I++ + KSVI+S A SY
Sbjct: 597 YLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSY 656
Query: 235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 294
+AQ R+DD D LT +R + L+ K++Q+R+E GAL LAS EVK +D+ET DP +
Sbjct: 657 EQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNE 716
Query: 295 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAA 351
+ + ++ N +VEEFML AN+SVA +I FP ++LRRH PS E+L +L T
Sbjct: 717 VEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRK 776
Query: 352 AVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHY 410
+ ++L+ SSKALADSLDR V +DPYFN L+RI++TRCM A YF SG + P+F HY
Sbjct: 777 NMSISLE--SSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHY 834
Query: 411 GLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQ 470
GLA +YTHFTSPIRRY DVV HR L+ ++G L +D+ ++ I N+N +HRNAQ
Sbjct: 835 GLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQ 894
Query: 471 MASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519
A R S+E + R + ++K+ +NG +V VPKFG+EG + L
Sbjct: 895 FAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRL 943
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
Length = 760
Score = 484 bits (1247), Expect = e-137, Method: Compositional matrix adjust.
Identities = 252/529 (47%), Positives = 338/529 (63%), Gaps = 19/529 (3%)
Query: 7 SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
S S + + D+ +PK+RI+TR+ LLDKRI++++DSW +YP GH+VR +G I
Sbjct: 175 SSSTQNVFVILXDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIE 234
Query: 67 DRDTESEMVLIDNDIDARPFSTQVLACLPPL------------PWSVSSEDLANPIRLDL 114
E+E +L+++D++ RPFS +VL CLP P +VS + L R DL
Sbjct: 235 SAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTK-RKDL 293
Query: 115 RDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSV 174
RD + S+DPPGC DI+DALH L +GN+EVGVHIADVT+FV PGT LD E + RGTSV
Sbjct: 294 RDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSV 353
Query: 175 YLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY 234
YLV++RID LP L D+CSL+ V+R AFSVIWEL A I++ + KSVI+S A SY
Sbjct: 354 YLVDKRIDXLPXLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFXKSVIRSREAFSY 413
Query: 235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 294
+AQ R+DD D LT R + L+ K++Q+R+E GAL LAS EVK D+ET DP +
Sbjct: 414 EQAQLRIDDKTQNDELTXGXRALLKLSVKLKQKRLEAGALNLASPEVKVHXDSETSDPNE 473
Query: 295 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAA 351
+ + ++ N +VEEF L AN+SVA +I FP + LRRH PS E+L L T
Sbjct: 474 VEIKKLLATNSLVEEFXLLANISVARKIYDAFPQTAXLRRHAAPPSTNFEILNEXLNTRK 533
Query: 352 AVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHY 410
++L+ SSKALADSLDR V +DPYFN L+RI +TRC A YF SG + P+F HY
Sbjct: 534 NXSISLE--SSKALADSLDRCVDPEDPYFNTLVRIXSTRCXXAAQYFYSGAYSYPDFRHY 591
Query: 411 GLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQ 470
GLA +YTHFTSPIRRY DVV HR L+ ++G L +D+ + I N+N +HRNAQ
Sbjct: 592 GLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKXDXICRNINRKHRNAQ 651
Query: 471 MASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519
A R S+E + R + ++K+ +NG +V VPKFG+EG + L
Sbjct: 652 FAGRASIEYYVGQVXRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRL 700
>pdb|2IX0|A Chain A, Rnase Ii
Length = 663
Score = 110 bits (276), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 132/470 (28%), Positives = 198/470 (42%), Gaps = 54/470 (11%)
Query: 110 IRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK 169
+R DL L ++D +D+DDAL AL ++ V IAD T ++ G+ LD A
Sbjct: 207 VREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKI 266
Query: 170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKS 228
R + YL I MLP+ L++D+CSLRA+ R + L+ + I + + + I+S
Sbjct: 267 RAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIES 326
Query: 229 CAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE---RGALTLASAEVKFQI 285
A L Y + ++++ P + + L ++ QRR E AL I
Sbjct: 327 KAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFI 386
Query: 286 DTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEP 345
E + LDI R AN++VEE M+AAN+ A ++LR + H +
Sbjct: 387 LGEKGEVLDIVAEPRRIANRIVEEAMIAANICAA-RVLRDKLGFGIYNVHMGFDPANADA 445
Query: 346 LLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNKLIRILATRCMTQAVYFCSGD 401
L GL++D L L R + P + + IR Q+ S +
Sbjct: 446 LAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRF------QSFAEISTE 499
Query: 402 LTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADN 461
P H+GL Y +TSPIR+Y D++ HRLL A + RPQ I
Sbjct: 500 PGP----HFGLGLEAYATWTSPIRKYGDMINHRLLKAV-----IKGETATRPQ-DEITVQ 549
Query: 462 LNYRHRNAQMASRGSVELHTLIYFR----KRPTDTE--ARIVKIR---------SNGFIV 506
+ R R +MA R ++ +Y R K TDT A IV I NG I
Sbjct: 550 MAERRRLNRMAER---DVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIA 606
Query: 507 FVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 556
F+P P R D V Q+ V++ G Y V +++
Sbjct: 607 FIP-----APFLHAVR------DELVCSQENGTVQIKGETVYKVTDVIDV 645
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
Length = 664
Score = 109 bits (272), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 131/470 (27%), Positives = 198/470 (42%), Gaps = 54/470 (11%)
Query: 110 IRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK 169
+R DL L ++D +D++DAL AL ++ V IAD T ++ G+ LD A
Sbjct: 208 VREDLTALDFVTIDSASTEDMNDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKI 267
Query: 170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKS 228
R + YL I MLP+ L++D+CSLRA+ R + L+ + I + + + I+S
Sbjct: 268 RAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIES 327
Query: 229 CAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE---RGALTLASAEVKFQI 285
A L Y + ++++ P + + L ++ QRR E AL I
Sbjct: 328 KAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFI 387
Query: 286 DTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEP 345
E + LDI R AN++VEE M+AAN+ A ++LR + H +
Sbjct: 388 LGEKGEVLDIVAEPRRIANRIVEEAMIAANICAA-RVLRDKLGFGIYNVHMGFDPANADA 446
Query: 346 LLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNKLIRILATRCMTQAVYFCSGD 401
L GL++D L L R + P + + IR Q+ S +
Sbjct: 447 LAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRF------QSFAEISTE 500
Query: 402 LTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADN 461
P H+GL Y +TSPIR+Y D++ HRLL A + RPQ I
Sbjct: 501 PGP----HFGLGLEAYATWTSPIRKYGDMINHRLLKAV-----IKGETATRPQ-DEITVQ 550
Query: 462 LNYRHRNAQMASRGSVELHTLIYFR----KRPTDTE--ARIVKIR---------SNGFIV 506
+ R R +MA R ++ +Y R K TDT A IV I NG I
Sbjct: 551 MAERRRLNRMAER---DVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIA 607
Query: 507 FVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 556
F+P P R D V Q+ V++ G Y V +++
Sbjct: 608 FIP-----APFLHAVR------DELVCSQENGTVQIKGETVYKVTDVIDV 646
>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 = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 132/488 (27%), Positives = 196/488 (40%), Gaps = 55/488 (11%)
Query: 98 PWSVSSEDLANP-IRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNF 156
P V++E L +R DL L ++D +D DDAL AL ++ V IAD T +
Sbjct: 175 PDGVATEXLDEGLVREDLTALDFVTIDSASTEDXDDALFAKALPDDKLQLIVAIADPTAW 234
Query: 157 VHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEI 216
+ G+ LD A R + YL I LP+ L++D+CSLRA+ R + L+ + I
Sbjct: 235 IAEGSKLDKAAKIRAFTNYLPGFNIPXLPRELSDDLCSLRANEVRPVLACRXTLSADGTI 294
Query: 217 I-STRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE---RG 272
+ + + I+S A L Y + ++++ P + + L ++ QRR E
Sbjct: 295 EDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNH 354
Query: 273 ALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLL 332
AL I E + LDI R AN++VEE A A ++LR +
Sbjct: 355 ALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEE-AXIAANICAARVLRDKLGFGIY 413
Query: 333 RRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNKLIRILAT 388
H + L GL++D L L R + P + + IR
Sbjct: 414 NVHXGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRF-- 471
Query: 389 RCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSV 448
Q+ S + P H+GL Y +TSPIR+Y D + HRLL A +
Sbjct: 472 ----QSFAEISTEPGP----HFGLGLEAYATWTSPIRKYGDXINHRLLKAV-----IKGE 518
Query: 449 FQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR----KRPTDTE--ARIVKIR-- 500
RPQ I R R + A R ++ +Y R K TDT A IV I
Sbjct: 519 TATRPQ-DEITVQXAERRRLNRXAER---DVGDWLYARFLKDKAGTDTRFAAEIVDISRG 574
Query: 501 -------SNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQT 553
NG I F+P P R D V Q+ V++ G Y V
Sbjct: 575 GXRVRLVDNGAIAFIP-----APFLHAVR------DELVCSQENGTVQIKGETVYKVTDV 623
Query: 554 VNIHMEVV 561
+++ + V
Sbjct: 624 IDVTIAEV 631
>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 = 73.6 bits (179), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 56/160 (35%), Positives = 82/160 (51%), Gaps = 7/160 (4%)
Query: 85 PFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNF 144
P++ ++ A L + V D A RLDL L F++D G +D DDA+ L G
Sbjct: 56 PYADRLRAALNAVELPVPDFDPAEE-RLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLT 114
Query: 145 EVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAF 204
+ VH+ADV V P +PLD EA RG ++YL +R I LP L +V A
Sbjct: 115 RLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGXLPDELVAKAGLGLHEVSP-AL 173
Query: 205 SVIWELTPE--AEIISTRYTKSVIKSCAALSYVEAQARMD 242
S+ +L P+ AE + T+ ++ L+Y EAQAR++
Sbjct: 174 SICLDLDPDGNAEAVDVLLTRVKVQR---LAYQEAQARLE 210
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 34/112 (30%), Positives = 48/112 (42%), Gaps = 15/112 (13%)
Query: 409 HYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTS--IADNLNYRH 466
H+G LY TSP RRY D+VVH+ L A L R L+S A ++
Sbjct: 327 HHGXGLDLYAQATSPXRRYLDLVVHQQLRAFLA---------GRDPLSSKVXAAHIAESQ 377
Query: 467 RNA---QMASRGSVELHTLIYFRKRPTDT-EARIVKIRSNGFIVFVPKFGIE 514
NA + A R S HTL + +P +A +V R + +P +
Sbjct: 378 XNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFD 429
>pdb|3MPI|A Chain A, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
Glutaryl-Coa Complex
pdb|3MPI|B Chain B, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
Glutaryl-Coa Complex
pdb|3MPI|C Chain C, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
Glutaryl-Coa Complex
pdb|3MPI|D Chain D, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
Glutaryl-Coa Complex
pdb|3MPJ|A Chain A, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
pdb|3MPJ|B Chain B, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
pdb|3MPJ|D Chain D, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
pdb|3MPJ|E Chain E, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
pdb|3MPJ|F Chain F, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
pdb|3MPJ|G Chain G, Structure Of The Glutaryl-Coenzyme A Dehydrogenase
Length = 397
Score = 36.2 bits (82), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 29/43 (67%)
Query: 24 KIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
++++ +++ N ++K+I+ D WD ++ +P+ VR +GE+G
Sbjct: 8 ELQMLQKEVRNFVNKKIVPFADQWDNENHFPYEEAVRPMGELG 50
>pdb|1VJV|A Chain A, Crystal Structure Of Ubiquitin Carboxyl-terminal Hydrolase
6 (yfr010w) From Saccharomyces Cerevisiae At 1.74 A
Resolution
Length = 415
Score = 32.3 bits (72), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 149 HIADVTNFVHPG--TPLDDEASKR-----GTSVYLVERRIDMLPKPLT 189
HI+ TNF G L+++ KR S+Y VE++I LPK LT
Sbjct: 180 HISGTTNFXRNGLLEGLNEKIEKRSDLTGANSIYSVEKKISRLPKFLT 227
>pdb|3ASY|A Chain A, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASY|B Chain B, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|A Chain A, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|B Chain B, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
Length = 211
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 415 PLYTHFTSPIRRYADVVVHR 434
P++ HF P +RYADV+V R
Sbjct: 167 PMHLHFVEPTKRYADVIVPR 186
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
0.321 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,519,891
Number of Sequences: 62578
Number of extensions: 676224
Number of successful extensions: 1401
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1376
Number of HSP's gapped (non-prelim): 11
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)