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= 007593
(597 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VJ7|A Chain A, Crystal Structure Of The Bifunctional Catalytic Fragment
Of Relseq, The RelaSPOT HOMOLOG FROM STREPTOCOCCUS
EQUISIMILIS.
pdb|1VJ7|B Chain B, Crystal Structure Of The Bifunctional Catalytic Fragment
Of Relseq, The RelaSPOT HOMOLOG FROM STREPTOCOCCUS
EQUISIMILIS
Length = 393
Score = 107 bits (266), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 52/125 (41%), Positives = 78/125 (62%), Gaps = 10/125 (8%)
Query: 176 GMEVTLSSRLKSLYSIFSKMRRKDVGIHKVYDARALRVVVGDKNGTLHGPAIQCCYSLLD 235
G+ + R K +YSI+ KMR K +++D A+R V+ ++ Y+++
Sbjct: 233 GLFGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSD---------VYAMVG 283
Query: 236 IVHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQGPDGSALEVQIRTQKMHEYAEHGLAAH 295
+H LW P+ G F DYI PK +GYQS+HT V GP G +E+QIRT++MH+ AE+G+AAH
Sbjct: 284 YIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGP-IEIQIRTKEMHQVAEYGVAAH 342
Query: 296 WLYKE 300
W YK+
Sbjct: 343 WAYKK 347
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 28/49 (57%)
Query: 9 LPPAKARAVAQETLLIWCSLASRLGLWALKAELEDLCFAVLQPQIFRKM 57
L K +++ET+ I+ LA RLG+ +K ELEDL F L F K+
Sbjct: 155 LRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYKI 203
>pdb|3L9D|A Chain A, The Crystal Structure Of Smu.1046c From Streptococcus
Mutans Ua159
pdb|3L9D|B Chain B, The Crystal Structure Of Smu.1046c From Streptococcus
Mutans Ua159
Length = 255
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 9/56 (16%)
Query: 250 DYIVNPKPSGYQSLHTAVQGP----DGSAL---EVQIRTQKMHEYA--EHGLAAHW 296
DYI N KPSGY+S H V+ P G + E+QIRT M+ +A EH L +
Sbjct: 138 DYINNLKPSGYRSYHVIVEYPVDTISGQRIIMAEIQIRTLAMNFWATIEHSLNYKY 193
>pdb|1RWS|A Chain A, Backbone Solution Structure Of Mixed AlphaBETA PROTEIN
PF1061
pdb|1SF0|A Chain A, Backbone Solution Structure Of Mixed AlphaBETA PROTEIN
PF1061
Length = 77
Score = 34.3 bits (77), Expect = 0.21, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 555 RSGSTAADAAMKVGL--EGKLVLVNGQLVLPNTELKDGDIVEV 595
R G D VG E + VNG++VL + E+KDGD VEV
Sbjct: 28 REGMKVRDILRAVGFNTESAIAKVNGKVVLEDDEVKDGDFVEV 70
>pdb|2BE3|A Chain A, Structure Of A Gtp Pyrophosphokinase Family Protein From
Streptococcus Pneumoniae
pdb|2BE3|B Chain B, Structure Of A Gtp Pyrophosphokinase Family Protein From
Streptococcus Pneumoniae
Length = 226
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 38/136 (27%), Positives = 58/136 (42%), Gaps = 26/136 (19%)
Query: 181 LSSRLKSLYSIFSKMRRKDVGI----HKVYDARALRVVVGDKNGTLHGPAIQCCYSLLDI 236
++ R+K + SI K R+ + H + D LRV V + ++DI
Sbjct: 45 VTGRVKPIESIKEKXARRGITYATLEHDLQDIAGLRVXV---------QFVDDVKEVVDI 95
Query: 237 VHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQ-------GPDGSALEVQIRTQKMHEYA- 288
+H+ + DYI + K SGY+S H V+ G E+QIRT + +A
Sbjct: 96 LHKRQDXRIIQERDYITHRKASGYRSYHVVVEYTVDTINGAKTILAEIQIRTLAXNFWAT 155
Query: 289 -EHGLAAHWLYKETGN 303
EH L YK G+
Sbjct: 156 IEHSLN----YKYQGD 167
>pdb|1RYJ|A Chain A, Solution Nmr Structure Of Protein Mth1743 From
Methanobacterium Thermoautotrophicum. Ontario Centre For
Structural Proteomics Target Mth1743_1_70; Northeast
Structural Genomics Consortium Target Tt526
Length = 70
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 565 MKVGLEGKLVLVNGQLVLPNTELKDGDIVEV 595
+++ +E +V NGQ+V+ E+ DGDI+EV
Sbjct: 33 LEIPIETVVVKKNGQIVIDEEEIFDGDIIEV 63
>pdb|1US4|A Chain A, Putative Glur0 Ligand Binding Core With L-Glutamate
Length = 314
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 174 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 217
IP E +++L +++ ++ RKD GI V D + RVVVGD
Sbjct: 91 IPAFEGKPVKTIRALAALYPEVVHVVARKDAGIRTVADLKGKRVVVGD 138
>pdb|1US5|A Chain A, Putative Glur0 Ligand Binding Core With L-Glutamate
Length = 314
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 174 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 217
IP E +++L +++ ++ RKD GI V D + RVVVGD
Sbjct: 91 IPAFEGKPVKTIRALAALYPEVVHVVARKDAGIRTVADLKGKRVVVGD 138
>pdb|2KMM|A Chain A, Solution Nmr Structure Of The Tgs Domain Of Pg1808 From
Porphyromonas Gingivalis. Northeast Structural Genomics
Consortium Target Pgr122a (418-481)
Length = 73
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 542 VIVCWPNGEIMRLRSGSTAADAAMK----VGLEGKLVLVNGQLVLPNTELKDGDIVEV 595
V+V P GEI RL G+TA D A +G VN +LV + L GD VEV
Sbjct: 3 VMVFTPKGEIKRLPQGATALDFAYSLHSDLGDHCIGAKVNHKLVPLSYVLNSGDQVEV 60
>pdb|2CU3|A Chain A, Crystal Structure Of Tt1568 From Thermus Thermophilus Hb8
pdb|2CU3|B Chain B, Crystal Structure Of Tt1568 From Thermus Thermophilus Hb8
pdb|2HTM|E Chain E, Crystal Structure Of Ttha0676 From Thermus Thermophilus
Hb8
pdb|2HTM|F Chain F, Crystal Structure Of Ttha0676 From Thermus Thermophilus
Hb8
pdb|2HTM|G Chain G, Crystal Structure Of Ttha0676 From Thermus Thermophilus
Hb8
pdb|2HTM|H Chain H, Crystal Structure Of Ttha0676 From Thermus Thermophilus
Hb8
Length = 64
Score = 30.0 bits (66), Expect = 3.7, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 546 WPNGEIMRLRSGSTAADAAMKVGLE--GKLVLVNGQ----LVLPNTELKDGDIVEV 595
W NGE R G T + + G+E G VL+N + L +P+ L+DGD+VEV
Sbjct: 3 WLNGE-PRPLEGKTLKEVLEEXGVELKGVAVLLNEEAFLGLEVPDRPLRDGDVVEV 57
>pdb|3CFW|A Chain A, L-selectin Lectin And Egf Domains
Length = 164
Score = 29.3 bits (64), Expect = 6.6, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 397 CWEAYARLYKKASDEWWCQPGHGDWCTCLEKYTL-CRDGMYHKQDQFGRLLPTFI 450
C + A L AS + W GHG+ + YT C G Y Q QF ++ P I
Sbjct: 109 CHKLKAALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVQVDPRLI 163
>pdb|2DI8|A Chain A, Solution Structure Of The 19th Filamin Domain From Human
Filamin-B
Length = 111
Score = 29.3 bits (64), Expect = 6.7, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 247 EFDDYIVNPKPSGYQSLHTAVQGPDGSALEVQIRTQKMHE 286
E D+IV+ + +GY + AV+GP +V I+T+ + +
Sbjct: 28 EMSDFIVDTRDAGYGGISLAVEGPS----KVDIQTEDLED 63
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
0.318 0.133 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,874,938
Number of Sequences: 62578
Number of extensions: 683817
Number of successful extensions: 1545
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1537
Number of HSP's gapped (non-prelim): 15
length of query: 597
length of database: 14,973,337
effective HSP length: 104
effective length of query: 493
effective length of database: 8,465,225
effective search space: 4173355925
effective search space used: 4173355925
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)