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= 009620
(530 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MUD|A Chain A, Structure Of The Tropomyosin Overlap Complex From Chicken
Smooth Muscle
pdb|3MUD|B Chain B, Structure Of The Tropomyosin Overlap Complex From Chicken
Smooth Muscle
Length = 175
Score = 32.3 bits (72), Expect = 0.71, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 36 RPVRCRLGNFSSYKVSRFCRKKRELICRVTDTQTEPDSNND--KEKEVHDGQEN 87
+ V RLG+F+ KV RELIC DT + + + D +EK H +EN
Sbjct: 105 KDVSFRLGSFNLEKVENPAEVIRELICYCLDTTAKNEKSIDDLEEKVAHAKEEN 158
>pdb|3RWR|A Chain A, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|B Chain B, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|F Chain F, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|G Chain G, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|J Chain J, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|K Chain K, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|N Chain N, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|P Chain P, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|R Chain R, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|V Chain V, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|U Chain U, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|Y Chain Y, Crystal Structure Of The Human Xrcc4-Xlf Complex
Length = 163
Score = 30.0 bits (66), Expect = 3.7, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 36 RPVRCRLGNFSSYKVSRFCRKKRELICRVTDTQTEPDSNND---KEKE 80
+ V RLG+F+ KV RELIC DT E + N+ KE E
Sbjct: 102 KDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNEHLQKENE 149
>pdb|3Q4F|C Chain C, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
pdb|3Q4F|D Chain D, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
pdb|3Q4F|G Chain G, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
pdb|3Q4F|H Chain H, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
Length = 186
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 36 RPVRCRLGNFSSYKVSRFCRKKRELICRVTDTQTEPDSNNDKEKEVHDGQENQ 88
+ V RLG+F+ KV RELIC DT E + N+ H +EN+
Sbjct: 131 KDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNE-----HLQKENE 178
>pdb|3II6|A Chain A, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|B Chain B, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|C Chain C, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|D Chain D, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv
Length = 203
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 36 RPVRCRLGNFSSYKVSRFCRKKRELICRVTDTQTEPDSNNDKEKEVHDGQENQ 88
+ V RLG+F+ KV RELIC DT E + N+ H +EN+
Sbjct: 102 KDVSFRLGSFNLEKVENPAEVIRELICYCLDTTAENQAKNE-----HLQKENE 149
>pdb|3B4R|A Chain A, Site-2 Protease From Methanocaldococcus Jannaschii
pdb|3B4R|B Chain B, Site-2 Protease From Methanocaldococcus Jannaschii
Length = 224
Score = 28.9 bits (63), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 42/178 (23%), Positives = 71/178 (39%), Gaps = 45/178 (25%)
Query: 274 LSTFDNLNLLTNGLPGALVTALV---IGVHELGHILAAKSTGVELGVPYFVPSWQIGSFG 330
L L+++ N + A++ L+ + +HELGH AK GV++ +P IG
Sbjct: 25 LVVIIGLSIMNNSIFWAVLFILLFVSVVLHELGHSYVAKKYGVKIEKILLLP---IGGVA 81
Query: 331 AITRIRNIVSKREDLLKVAAAGPLAXXXXXXXXXXXXXXXPPSDGIGIVVDASVFHESXX 390
+ +I +E L++ AGPL GI +++ + F
Sbjct: 82 MMDKI-----PKEGELRIGIAGPLVSFII---------------GIVLLIVSQFF----- 116
Query: 391 XXXXXXXXXXDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRK 448
D+ +G P+ ++ G N IPA +DGGRI A+ +K
Sbjct: 117 ----------DININGYPLLYTLSLLNLMLG----GFNLIPAFPMDGGRILRAILSKK 160
>pdb|3W03|C Chain C, Xlf-Xrcc4 Complex
pdb|3W03|D Chain D, Xlf-Xrcc4 Complex
Length = 184
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 36 RPVRCRLGNFSSYKVSRFCRKKRELICRVTDTQTEPDSNNDKEKEVHDGQENQ 88
+ V RLG+F+ KV RELIC DT E + N+ H +EN+
Sbjct: 122 KDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNE-----HLQKENE 169
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
0.319 0.138 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,164,597
Number of Sequences: 62578
Number of extensions: 541244
Number of successful extensions: 935
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 931
Number of HSP's gapped (non-prelim): 8
length of query: 530
length of database: 14,973,337
effective HSP length: 103
effective length of query: 427
effective length of database: 8,527,803
effective search space: 3641371881
effective search space used: 3641371881
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)