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= 002340
(934 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QSH|A Chain A, Crystal Structure Of Rad4-Rad23 Bound To A Mismatch Dna
Length = 538
Score = 89.7 bits (221), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 85/344 (24%), Positives = 140/344 (40%), Gaps = 54/344 (15%)
Query: 482 VGAPLYWAEVYCSGENLTGKWVHVDAANAI----IDGEQKVEAAAAAC--KTSLRYIVAF 535
V P++W EV+ + + KW+ VD N + K+ AC + LRY++A+
Sbjct: 216 VKYPIFWCEVW---DKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAY 272
Query: 536 -AGCGAKDVTRRYCMKWY-------RIASKRVNSAWWDAVLAPLRELESGATGDLNVESS 587
G +DVTRRY +W RI W+ V+ L + D
Sbjct: 273 DRKYGCRDVTRRYA-QWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDY----- 326
Query: 588 AKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGF 647
ED R +E +P + Q KNH YV+E+ + + QI+ P G+
Sbjct: 327 ------------EDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGY 374
Query: 648 CSGHA-------VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPE 700
H VY + + LK+ +W +K G E E
Sbjct: 375 LKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAE 431
Query: 701 DYDE-VDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPR 759
+ DE + + + ELY + PL ++ +G + +N G ++V++ +P + P
Sbjct: 432 EEDERLYSFEDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPV 484
Query: 760 VYSVAKRLEIDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 802
A+ L ++ APA+ F+F G + PV GIVV ++ I
Sbjct: 485 AIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAI 528
>pdb|2QSF|A Chain A, Crystal Structure Of The Rad4-Rad23 Complex
pdb|2QSG|A Chain A, Crystal Structure Of Rad4-Rad23 Bound To A Uv-Damaged Dna
Length = 533
Score = 89.7 bits (221), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 85/344 (24%), Positives = 140/344 (40%), Gaps = 54/344 (15%)
Query: 482 VGAPLYWAEVYCSGENLTGKWVHVDAANAI----IDGEQKVEAAAAAC--KTSLRYIVAF 535
V P++W EV+ + + KW+ VD N + K+ AC + LRY++A+
Sbjct: 211 VKYPIFWCEVW---DKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAY 267
Query: 536 -AGCGAKDVTRRYCMKWY-------RIASKRVNSAWWDAVLAPLRELESGATGDLNVESS 587
G +DVTRRY +W RI W+ V+ L + D
Sbjct: 268 DRKYGCRDVTRRYA-QWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDY----- 321
Query: 588 AKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGF 647
ED R +E +P + Q KNH YV+E+ + + QI+ P G+
Sbjct: 322 ------------EDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGY 369
Query: 648 CSGHA-------VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPE 700
H VY + + LK+ +W +K G E E
Sbjct: 370 LKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAE 426
Query: 701 DYDE-VDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPR 759
+ DE + + + ELY + PL ++ +G + +N G ++V++ +P + P
Sbjct: 427 EEDERLYSFEDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPV 479
Query: 760 VYSVAKRLEIDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 802
A+ L ++ APA+ F+F G + PV GIVV ++ I
Sbjct: 480 AIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAI 523
>pdb|2F4M|A Chain A, The Mouse Pngase-Hr23 Complex Reveals A Complete
Remodulation Of The Protein-Protein Interface Compared
To Its Yeast Orthologs
pdb|2F4O|A Chain A, The Mouse Pngase-Hr23 Complex Reveals A Complete
Remodulation Of The Protein-Protein Interface Compared
To Its Yeast Orthologs
Length = 295
Score = 35.4 bits (80), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 488 WAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRY 547
W EVY + +W+H DA + D E L YI+AF+ DVT RY
Sbjct: 172 WTEVYSPSQQ---RWLHCDACEDVCDKPLLYEIGWGK---KLSYIIAFSKDEVVDVTWRY 225
Query: 548 CMKWYRIASKR 558
K + S+R
Sbjct: 226 SCKHDEVMSRR 236
>pdb|3ESW|A Chain A, Complex Of Yeast Pngase With Glcnac2-Iac
Length = 355
Score = 34.3 bits (77), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 29/132 (21%), Positives = 49/132 (37%), Gaps = 11/132 (8%)
Query: 423 EMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKV 482
E + V K N C ++ + P+K L+ G C + + S +
Sbjct: 166 ESKFNCGTVEIYKCNRCGNITRFPRYND---PIKLLE-TRKGRXGEWCNLFTLILKSFGL 221
Query: 483 GAPLYWA---EVYCS-GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGC 538
W V+C N +WVHVD+ D + + + Y +AF
Sbjct: 222 DVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFD---QPYIYSINWNKKMSYCIAFGKD 278
Query: 539 GAKDVTRRYCMK 550
G DV++RY ++
Sbjct: 279 GVVDVSKRYILQ 290
>pdb|1X3Z|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 33.9 bits (76), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 29/132 (21%), Positives = 49/132 (37%), Gaps = 11/132 (8%)
Query: 423 EMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKV 482
E + V K N C ++ + P+K L+ G C + + S +
Sbjct: 145 ESKFNCGTVEIYKCNRCGNITRFPRYND---PIKLLE-TRKGRCGEWCNLFTLILKSFGL 200
Query: 483 GAPLYWA---EVYCS-GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGC 538
W V+C N +WVHVD+ D + + + Y +AF
Sbjct: 201 DVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFD---QPYIYSINWNKKMSYCIAFGKD 257
Query: 539 GAKDVTRRYCMK 550
G DV++RY ++
Sbjct: 258 GVVDVSKRYILQ 269
>pdb|1X3W|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 33.1 bits (74), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 51/132 (38%), Gaps = 11/132 (8%)
Query: 423 EMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKV 482
E + V K N C ++ + P+K L+ G C + + S +
Sbjct: 145 ESKFNCGTVEIYKCNRCGNITRFPRYND---PIKLLE-TRKGRCGEWCNLFTLILKSFGL 200
Query: 483 GAPLYWA---EVYCS-GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGC 538
W V+C N +WVHVD+ D + + + K S Y +AF
Sbjct: 201 DVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFD-QPYIYSINWNKKXS--YCIAFGKD 257
Query: 539 GAKDVTRRYCMK 550
G DV++RY ++
Sbjct: 258 GVVDVSKRYILQ 269
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
0.313 0.128 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,270,832
Number of Sequences: 62578
Number of extensions: 988085
Number of successful extensions: 1635
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1625
Number of HSP's gapped (non-prelim): 11
length of query: 934
length of database: 14,973,337
effective HSP length: 108
effective length of query: 826
effective length of database: 8,214,913
effective search space: 6785518138
effective search space used: 6785518138
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)