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= 006346
(649 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 = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 93/215 (43%), Gaps = 19/215 (8%)
Query: 312 NSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHA---- 367
+ ED R +E +P + Q KNH YV+E+ + + QI+ P G+ H
Sbjct: 324 DDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGK 383
Query: 368 ---VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPEDYDE-VDAR 423
VY + + LK+ +W +K G E E+ DE + +
Sbjct: 384 VLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAEEEDERLYSF 440
Query: 424 GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLE 483
+ ELY + PL ++ +G + +N G ++V++ +P + P A+ L
Sbjct: 441 EDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLG 493
Query: 484 IDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 517
++ APA+ F+F G + PV GIVV ++ I
Sbjct: 494 VEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAI 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 = 62.4 bits (150), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 93/215 (43%), Gaps = 19/215 (8%)
Query: 312 NSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHA---- 367
+ ED R +E +P + Q KNH YV+E+ + + QI+ P G+ H
Sbjct: 319 DDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGK 378
Query: 368 ---VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPEDYDE-VDAR 423
VY + + LK+ +W +K G E E+ DE + +
Sbjct: 379 VLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAEEEDERLYSF 435
Query: 424 GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLE 483
+ ELY + PL ++ +G + +N G ++V++ +P + P A+ L
Sbjct: 436 EDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLG 488
Query: 484 IDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 517
++ APA+ F+F G + PV GIVV ++ I
Sbjct: 489 VEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAI 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 = 0.091, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 163 WAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRY 222
W EVY + +W+H DA + D E L YI+AF+ DVT RY
Sbjct: 172 WTEVYSPSQQ---RWLHCDACEDVCDKPLLYEIGWGK---KLSYIIAFSKDEVVDVTWRY 225
Query: 223 CMKWYRIASKR 233
K + S+R
Sbjct: 226 SCKHDEVMSRR 236
>pdb|3ESW|A Chain A, Complex Of Yeast Pngase With Glcnac2-Iac
Length = 355
Score = 33.5 bits (75), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 29/132 (21%), Positives = 49/132 (37%), Gaps = 11/132 (8%)
Query: 98 EMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKV 157
E + V K N C ++ + P+K L+ G C + + S +
Sbjct: 166 ESKFNCGTVEIYKCNRCGNITRFPRYND---PIKLLE-TRKGRXGEWCNLFTLILKSFGL 221
Query: 158 GAPLYWA---EVYCS-GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGC 213
W V+C N +WVHVD+ D + + + Y +AF
Sbjct: 222 DVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFD---QPYIYSINWNKKMSYCIAFGKD 278
Query: 214 GAKDVTRRYCMK 225
G DV++RY ++
Sbjct: 279 GVVDVSKRYILQ 290
>pdb|1X3Z|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 29/132 (21%), Positives = 49/132 (37%), Gaps = 11/132 (8%)
Query: 98 EMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKV 157
E + V K N C ++ + P+K L+ G C + + S +
Sbjct: 145 ESKFNCGTVEIYKCNRCGNITRFPRYND---PIKLLE-TRKGRCGEWCNLFTLILKSFGL 200
Query: 158 GAPLYWA---EVYCS-GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGC 213
W V+C N +WVHVD+ D + + + Y +AF
Sbjct: 201 DVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFD---QPYIYSINWNKKMSYCIAFGKD 257
Query: 214 GAKDVTRRYCMK 225
G DV++RY ++
Sbjct: 258 GVVDVSKRYILQ 269
>pdb|1X3W|A Chain A, Structure Of A Peptide:n-Glycanase-Rad23 Complex
Length = 335
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 51/132 (38%), Gaps = 11/132 (8%)
Query: 98 EMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKV 157
E + V K N C ++ + P+K L+ G C + + S +
Sbjct: 145 ESKFNCGTVEIYKCNRCGNITRFPRYND---PIKLLE-TRKGRCGEWCNLFTLILKSFGL 200
Query: 158 GAPLYWA---EVYCS-GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGC 213
W V+C N +WVHVD+ D + + + K S Y +AF
Sbjct: 201 DVRYVWNREDHVWCEYFSNFLNRWVHVDSCEQSFD-QPYIYSINWNKKXS--YCIAFGKD 257
Query: 214 GAKDVTRRYCMK 225
G DV++RY ++
Sbjct: 258 GVVDVSKRYILQ 269
>pdb|3VFD|A Chain A, Human Spastin Aaa Domain
Length = 389
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 240 DAVLAPLRELESGATGGMTQMEKRHVNASNILEALK 275
DA L P+REL+ M+ E R++ S+ E+LK
Sbjct: 328 DAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLK 363
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 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,855,184
Number of Sequences: 62578
Number of extensions: 692533
Number of successful extensions: 1162
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1153
Number of HSP's gapped (non-prelim): 8
length of query: 649
length of database: 14,973,337
effective HSP length: 105
effective length of query: 544
effective length of database: 8,402,647
effective search space: 4571039968
effective search space used: 4571039968
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: 55 (25.8 bits)