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= psy15374
(205 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2A1I|A Chain A, Crystal Structure Of The Central Domain Of Human Ercc1
Length = 146
Score = 167 bits (424), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 78/130 (60%), Positives = 102/130 (78%), Gaps = 6/130 (4%)
Query: 68 SNAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADR 127
SN+I+V+PRQ+GNP+LK + VPWE+ D +IPDYV+G++TCALFLS++YH L PDYI R
Sbjct: 17 SNSIIVSPRQRGNPVLKFVRNVPWEFGD-VIPDYVLGQSTCALFLSLRYHNLHPDYIHGR 75
Query: 128 IKALGKLYKL-----QVDSKDPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYKVFE 182
+++LGK + L QVD KDP ALK L ++C+L D TL+LAWSPEEAG +ETYK +E
Sbjct: 76 LQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYE 135
Query: 183 NKPPDLIMEK 192
KP DL+MEK
Sbjct: 136 QKPADLLMEK 145
Score = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 21/30 (70%), Positives = 25/30 (83%)
Query: 1 MLAWSPEEAGEMIETYKVFENKPPDLIMEK 30
+LAWSPEEAG +ETYK +E KP DL+MEK
Sbjct: 116 ILAWSPEEAGRYLETYKAYEQKPADLLMEK 145
>pdb|2JPD|A Chain A, Solution Structure Of The Ercc1 Central Domain
Length = 135
Score = 159 bits (401), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 74/126 (58%), Positives = 97/126 (76%), Gaps = 6/126 (4%)
Query: 68 SNAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADR 127
SN+I+V+PRQ+GNP+LK + VPWE+ D +IPDYV+G++TCALFLS++YH L PDYI R
Sbjct: 4 SNSIIVSPRQRGNPVLKFVRNVPWEFGD-VIPDYVLGQSTCALFLSLRYHNLHPDYIHGR 62
Query: 128 IKALGKLYKL-----QVDSKDPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYKVFE 182
+++LGK + L QVD KDP ALK L ++C+L D TL+LAWSPEEAG +ETYK +E
Sbjct: 63 LQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYE 122
Query: 183 NKPPDL 188
KP L
Sbjct: 123 QKPGGL 128
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/26 (65%), Positives = 20/26 (76%)
Query: 1 MLAWSPEEAGEMIETYKVFENKPPDL 26
+LAWSPEEAG +ETYK +E KP L
Sbjct: 103 ILAWSPEEAGRYLETYKAYEQKPGGL 128
>pdb|2JNW|A Chain A, Solution Structure Of A Ercc1-Xpa Heterodimer
Length = 133
Score = 150 bits (379), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 70/117 (59%), Positives = 92/117 (78%), Gaps = 6/117 (5%)
Query: 68 SNAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADR 127
SN+I+V+PRQ+GNP+LK + VPWE+ D +IPDYV+G++TCALFLS++YH L PDYI R
Sbjct: 17 SNSIIVSPRQRGNPVLKFVRNVPWEFGD-VIPDYVLGQSTCALFLSLRYHNLHPDYIHGR 75
Query: 128 IKALGKLYKL-----QVDSKDPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYK 179
+++LGK + L QVD KDP ALK L ++C+L D TL+LAWSPEEAG +ETYK
Sbjct: 76 LQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYK 132
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/17 (76%), Positives = 15/17 (88%)
Query: 1 MLAWSPEEAGEMIETYK 17
+LAWSPEEAG +ETYK
Sbjct: 116 ILAWSPEEAGRYLETYK 132
>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana
pdb|1U3D|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana With Amppnp Bound
Length = 509
Score = 30.8 bits (68), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 33/83 (39%), Gaps = 3/83 (3%)
Query: 50 NSATSESVQP--SRAGASKSSNAILVN-PRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRT 106
N A ESV G + S I N P PLL H+ PW D++ + GRT
Sbjct: 280 NEAGEESVNLFLKSIGLREYSRYISFNHPYSHERPLLGHLKFFPWAVDENYFKAWRQGRT 339
Query: 107 TCALFLSIKYHALKPDYIADRIK 129
L + ++ DRI+
Sbjct: 340 GYPLVDAGMRELWATGWLHDRIR 362
>pdb|3PHZ|A Chain A, Crystal Structure Analysis Of Polyporus Squamosus Lectin
Bound To Human-Type Influenza-Binding Epitope
Neu5aca2-6galb1-4glcnac
pdb|3PHZ|B Chain B, Crystal Structure Analysis Of Polyporus Squamosus Lectin
Bound To Human-Type Influenza-Binding Epitope
Neu5aca2-6galb1-4glcnac
Length = 286
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 21 NKPPDLIMEKQDVDPHSKTWNFDPVPAAQNSATSESVQPSR---AGASKSSNAILVNPRQ 77
NK PD+I+ VDP + W +PV A + S AG + + ++ R
Sbjct: 30 NKSPDVIISSDAVDPLNNLWLIEPVGEADTYTVRNAFAGSYMDLAGHAATDGTAIIGYRP 89
Query: 78 KGNPLLKHI 86
G K I
Sbjct: 90 TGGDNQKWI 98
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
0.316 0.133 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,850,407
Number of Sequences: 62578
Number of extensions: 272789
Number of successful extensions: 677
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 660
Number of HSP's gapped (non-prelim): 12
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
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: 49 (23.5 bits)