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= 044490
(430 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AAF|A Chain A, Structure Of Wrn Rqc Domain Bound To Double-Stranded Dna
pdb|3AAF|B Chain B, Structure Of Wrn Rqc Domain Bound To Double-Stranded Dna
Length = 134
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 47/81 (58%), Gaps = 4/81 (4%)
Query: 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIK--DVYRTVSVSQQGKQ 58
S+++ D Q+ + L G GKD + +WWK + QLI+ G+L E + + +++++G+
Sbjct: 46 SQRLAD-QYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICALTKKGRN 104
Query: 59 YLGSARPDHQPPLLLTFNGEM 79
+L A + Q L+L N E+
Sbjct: 105 WLHKANTESQ-SLILQANEEL 124
>pdb|2AXL|A Chain A, Solution Structure Of A Multifunctional Dna- And Protein-
Binding Domain Of Human Werner Syndrome Protein
Length = 144
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 47/81 (58%), Gaps = 4/81 (4%)
Query: 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIK--DVYRTVSVSQQGKQ 58
S+++ D Q+ + L G GKD + +WWK + QLI+ G+L E + + +++++G+
Sbjct: 43 SQRLAD-QYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICALTKKGRN 101
Query: 59 YLGSARPDHQPPLLLTFNGEM 79
+L A + Q L+L N E+
Sbjct: 102 WLHKANTESQ-SLILQANEEL 121
>pdb|2E1E|A Chain A, Crystal Structure Of The Hrdc Domain Of Human Werner
Syndrome Protein, Wrn
pdb|2E1F|A Chain A, Crystal Structure Of The Hrdc Domain Of Human Werner
Syndrome Protein, Wrn
Length = 103
Score = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 108 EADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVI 167
E + LY L+E R+K A P L ++ + +A RP+T + IDGV++
Sbjct: 12 ETQIVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAA 71
Query: 168 THGDHLLQTIRHLSQKLNLSLD 189
LL+ I+H Q ++ D
Sbjct: 72 MLAP-LLEVIKHFCQTNSVQTD 92
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETI 43
++++ D DKL ++G+G+D S W ++ QLI G +T+ I
Sbjct: 444 NQRIRDYGHDKLKVYGMGRDKSHEHWVSVIRQLIHLGLVTQNI 486
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%)
Query: 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETI 43
++++ D DKL ++G G+D S W ++ QLI G +T+ I
Sbjct: 444 NQRIRDYGHDKLKVYGXGRDKSHEHWVSVIRQLIHLGLVTQNI 486
>pdb|2DGZ|A Chain A, Solution Structure Of The Helicase And Rnase D C-Terminal
Domain In Werner Syndrome Atp-Dependent Helicase
Length = 113
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 108 EADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVI 167
E + LY L+E R+K A P L ++ + +A RP+T + IDGV++
Sbjct: 19 ETQIVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAA 78
Query: 168 THGDHLLQTIRHLSQKLNLSLD 189
L + I+H Q ++ D
Sbjct: 79 MLAP-LWEVIKHFCQTNSVQTD 99
>pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium
Adolescentis
Length = 440
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 111 MQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVI--- 167
+ + L R +LAR AP L D +I ++A +P A+ +I +N+ + I
Sbjct: 234 LAIVRALWTRRDELAREYDIAPTLLLSDSSIIEVAKRKPHNAAQFRSIRSINERVRIHTD 293
Query: 168 THGDHLLQTIRHLSQKLNLSL 188
+ D + + + +K+ S+
Sbjct: 294 SEQDKMFERYAPIQRKIKPSM 314
>pdb|2KV2|A Chain A, Solution Structure Of The Human Blm Hrdc Domain
Length = 85
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%)
Query: 117 LLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQT 176
L E K L +V G + + T+KK+A + S L IDGV + + +G ++
Sbjct: 13 LTEVCKSLGKVFGVHYFNIFNTVTLKKLAESLSSDPEVLLQIDGVTEDKLEKYGAEVISV 72
Query: 177 IRHLSQ 182
++ S+
Sbjct: 73 LQKYSE 78
>pdb|1WUD|A Chain A, E. Coli Recq Hrdc Domain
pdb|1WUD|B Chain B, E. Coli Recq Hrdc Domain
pdb|1WUD|D Chain D, E. Coli Recq Hrdc Domain
Length = 89
Score = 29.6 bits (65), Expect = 3.4, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 31/69 (44%)
Query: 110 DMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITH 169
D +L+ L + RK +A + PY + D T+ + A P T + +++GV +
Sbjct: 12 DRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEXAEQXPITASEXLSVNGVGXRKLERF 71
Query: 170 GDHLLQTIR 178
G IR
Sbjct: 72 GKPFXALIR 80
>pdb|2RRD|A Chain A, Structure Of Hrdc Domain From Human Bloom Syndrome
Protein, Blm
Length = 101
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%)
Query: 117 LLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQT 176
L E K L +V G + + T+KK+A + S L IDGV + + +G ++
Sbjct: 28 LTEVCKSLGKVFGVHYFNIFNTVTLKKLAESLSSDPEVLLQIDGVTEDKLEKYGAEVISV 87
Query: 177 IRHLSQ 182
++ S+
Sbjct: 88 LQKYSE 93
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
0.314 0.131 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,092,982
Number of Sequences: 62578
Number of extensions: 540804
Number of successful extensions: 954
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 944
Number of HSP's gapped (non-prelim): 11
length of query: 430
length of database: 14,973,337
effective HSP length: 102
effective length of query: 328
effective length of database: 8,590,381
effective search space: 2817644968
effective search space used: 2817644968
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)