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= 000814
(1269 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 57.0 bits (136), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 52/205 (25%), Positives = 85/205 (41%), Gaps = 25/205 (12%)
Query: 122 PSTNGQTAQVAMXXXXXXXXMTPTIFYASRTHSQISQVISEYKK--TAYRVPMAVLASRK 179
P+ +G+T + Y RT+SQ QVI E + + ++ + R
Sbjct: 12 PTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRV 71
Query: 180 HYCT-NKYVRDKENIDEE-----CKL----LLGDRNLGCPQFKNVHKVRGHPSLQKGGCH 229
+ C + V D I+ E C + ++ CP F K+R + ++
Sbjct: 72 NMCILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFN--FKIRSDET-KRFLFD 128
Query: 230 EVHDIEDLVNVGQVVRGCSYYAARSMADDAQLVFCPYSYIINPVIRGAME-------VDI 282
E+ E+ + G+ C Y + ++ DA +V PY+Y +N R E V
Sbjct: 129 ELPTAEEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLN---RSVAEKFLSHWGVSR 185
Query: 283 KGAILILDEAHNIEDIARDAGSVDI 307
++ILDEAHN+ DI R GS I
Sbjct: 186 NQIVIILDEAHNLPDIGRSIGSFRI 210
Score = 37.0 bits (84), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 634 IVVGIPFPNINDIQVSLKKKYNDTYRSSKNLLSGNEWYCNQAFRA---LNQAIGRCIRHR 690
I+ G+PFP + I SL Y Y G W + + + Q IGR IR
Sbjct: 503 ILAGLPFPRPDAINRSLFDYYERKY--------GKGWEYSVVYPTAIKIRQEIGRLIRSA 554
Query: 691 FDYGAIILLDER 702
D GA ++LD+R
Sbjct: 555 EDTGACVILDKR 566
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 57.0 bits (136), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 52/205 (25%), Positives = 85/205 (41%), Gaps = 25/205 (12%)
Query: 122 PSTNGQTAQVAMXXXXXXXXMTPTIFYASRTHSQISQVISEYKK--TAYRVPMAVLASRK 179
P+ +G+T + Y RT+SQ QVI E + + ++ + R
Sbjct: 30 PTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRV 89
Query: 180 HYCT-NKYVRDKENIDEE-----CKL----LLGDRNLGCPQFKNVHKVRGHPSLQKGGCH 229
+ C + V D I+ E C + ++ CP F K+R + ++
Sbjct: 90 NMCILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFN--FKIRSDET-KRFLFD 146
Query: 230 EVHDIEDLVNVGQVVRGCSYYAARSMADDAQLVFCPYSYIINPVIRGAME-------VDI 282
E+ E+ + G+ C Y + ++ DA +V PY+Y +N R E V
Sbjct: 147 ELPTAEEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLN---RSVAEKFLSHWGVSR 203
Query: 283 KGAILILDEAHNIEDIARDAGSVDI 307
++ILDEAHN+ DI R GS I
Sbjct: 204 NQIVIILDEAHNLPDIGRSIGSFRI 228
Score = 37.0 bits (84), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 634 IVVGIPFPNINDIQVSLKKKYNDTYRSSKNLLSGNEWYCNQAFRA---LNQAIGRCIRHR 690
I+ G+PFP + I SL Y Y G W + + + Q IGR IR
Sbjct: 521 ILAGLPFPRPDAINRSLFDYYERKY--------GKGWEYSVVYPTAIKIRQEIGRLIRSA 572
Query: 691 FDYGAIILLDER 702
D GA ++LD+R
Sbjct: 573 EDTGACVILDKR 584
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 35.4 bits (80), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 634 IVVGIPFPNINDIQVSLKKKYNDTYRSSKNLLSGNEWYCNQ--AFRALNQAIGRCIRHRF 691
++VGIP+P +D L + R S + NE + + A + QAIGR IR
Sbjct: 467 VIVGIPYPPPDDYLKILAQ------RVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVN 520
Query: 692 DYGAIILLDERFQ 704
D + LLD+RF+
Sbjct: 521 DKCNVWLLDKRFE 533
Score = 34.7 bits (78), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 30/54 (55%)
Query: 245 RGCSYYAARSMADDAQLVFCPYSYIINPVIRGAMEVDIKGAILILDEAHNIEDI 298
+ C YY+ + A ++ Y Y R +++D++ ++++DEAHN++ +
Sbjct: 135 KFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDKV 188
>pdb|2AEZ|A Chain A, Crystal Structure Of Fructan 1-Exohydrolase Iia (E201q)
From Cichorium Intybus In Complex With 1-Kestose
Length = 543
Score = 34.7 bits (78), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 684 GRCIRHRFDYGAIILLDERFQEERNRAHISKWLRKSIKQYDSFDASLEGLKSFFRDVKGW 743
G + R+DYG F + +NR + W+ ++ Q D + GL+SF R + W
Sbjct: 261 GSTLDLRYDYGQFYASKSFFDDAKNRRVLWAWVPETDSQADDIEKGWAGLQSFPRAL--W 318
Query: 744 VGKKMFNGLENSDNDVDHVSSMDQCKEVTKQN 775
+ + NG + V+ + + Q +V QN
Sbjct: 319 IDR---NGKQLIQWPVEEIEELRQ-NQVNLQN 346
>pdb|1ST8|A Chain A, Crystal Structure Of Fructan 1-Exohydrolase Iia From
Cichorium Intybus
pdb|2ADD|A Chain A, Crystal Structure Of Fructan 1-Exohydrolase Iia From
Cichorium Intybus In Complex With Sucrose
pdb|2ADE|A Chain A, Crystal Structure Of Fructan 1-Exohydrolase Iia From
Cichorium Intybus In Complex With Fructose
pdb|2AEY|A Chain A, Crystal Structure Of Fructan 1-Exohydrolase Iia From
Cichorium Intybus In Complex With 2,5
Dideoxy-2,5-Immino-D-Mannitol
Length = 543
Score = 34.7 bits (78), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 684 GRCIRHRFDYGAIILLDERFQEERNRAHISKWLRKSIKQYDSFDASLEGLKSFFRDVKGW 743
G + R+DYG F + +NR + W+ ++ Q D + GL+SF R + W
Sbjct: 261 GSTLDLRYDYGQFYASKSFFDDAKNRRVLWAWVPETDSQADDIEKGWAGLQSFPRAL--W 318
Query: 744 VGKKMFNGLENSDNDVDHVSSMDQCKEVTKQN 775
+ + NG + V+ + + Q +V QN
Sbjct: 319 IDR---NGKQLIQWPVEEIEELRQ-NQVNLQN 346
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 11/75 (14%)
Query: 21 GGIQVEFPYQPYGSQLVFMCRVISTLDRAQRDGHCHALLESPTGTGKSLSLL-------C 73
G Q+ PY+P G Q + +++ L R G H L TGTGK+ ++
Sbjct: 3 GRFQLVAPYEPQGDQPQAIAKLVDGL----RRGVKHQTLLGATGTGKTFTISNVIAQVNK 58
Query: 74 STLAWQQNCKLKNQL 88
TL N L QL
Sbjct: 59 PTLVIAHNKTLAGQL 73
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 11/75 (14%)
Query: 21 GGIQVEFPYQPYGSQLVFMCRVISTLDRAQRDGHCHALLESPTGTGKSLSLL-------C 73
G Q+ PY+P G Q + +++ L R G H L TGTGK+ ++
Sbjct: 3 GRFQLVAPYEPQGDQPQAIAKLVDGL----RRGVKHQTLLGATGTGKTFTISNVIAQVNK 58
Query: 74 STLAWQQNCKLKNQL 88
TL N L QL
Sbjct: 59 PTLVIAHNKTLAGQL 73
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 21 GGIQVEFPYQPYGSQLVFMCRVISTLDRAQRDGHCHALLESPTGTGKSLSL 71
G Q+ PY+P G Q + +++ L R G H L TGTGK+ ++
Sbjct: 3 GRFQLVAPYEPQGDQPQAIAKLVDGL----RRGVKHQTLLGATGTGKTFTI 49
>pdb|2VL7|A Chain A, Structure Of S. Tokodaii Xpd4
Length = 540
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 634 IVVGIPFPNINDIQVSLKKKYNDTYRSSKNLLSGNE---WYCNQAFRALNQAIGRCIRHR 690
++ G+P+PN++D V +K+ R SK L+G + + + Q IGR R
Sbjct: 457 VLAGLPYPNVSDDMV--RKRIE---RLSK--LTGKDEDSIIHDLTAIVIKQTIGRAFRDP 509
Query: 691 FDYGAIILLDERFQE 705
DY I L D R++E
Sbjct: 510 NDYVKIYLCDSRYRE 524
Score = 31.6 bits (70), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 247 CSYYAARSMADDAQLVFCPYSYIINPVIRGAME------VDIKGAILILDEAHNI 295
C YY+ R+ D ++ Y Y+ IR ++ + ++ ++++DEAHN+
Sbjct: 133 CPYYSLRANLKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNL 187
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And
Processing By Uvrb: Crystal Structure Of A UvrbDNA
COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And
Processing By Uvrb: Crystal Structure Of A UvrbDNA
COMPLEX
Length = 658
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 21 GGIQVEFPYQPYGSQLVFMCRVISTLDRAQRDGHCHALLESPTGTGKSLSL 71
G Q+ PY+P G Q + +++ L R G H L TGTGK+ ++
Sbjct: 3 GRFQLVAPYEPQGDQPQAIAKLVDGL----RRGVKHQTLLGATGTGKTFTI 49
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
0.315 0.130 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 36,737,418
Number of Sequences: 62578
Number of extensions: 1480874
Number of successful extensions: 3527
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 3500
Number of HSP's gapped (non-prelim): 23
length of query: 1269
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1159
effective length of database: 8,089,757
effective search space: 9376028363
effective search space used: 9376028363
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.6 bits)