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= 005392
(698 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 (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 52/125 (41%), Positives = 78/125 (62%), Gaps = 10/125 (8%)
Query: 277 GMEVTLSSRLKSLYSIFSKMRRKDVGIHKVYDARALRVVVGDKNGTLHGPAIQCCYSLLD 336
G+ + R K +YSI+ KMR K +++D A+R V+ ++ Y+++
Sbjct: 233 GLFGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSD---------VYAMVG 283
Query: 337 IVHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQGPDGSALEVQIRTQKMHEYAEHGLAAH 396
+H LW P+ G F DYI PK +GYQS+HT V GP G +E+QIRT++MH+ AE+G+AAH
Sbjct: 284 YIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGP-IEIQIRTKEMHQVAEYGVAAH 342
Query: 397 WLYKE 401
W YK+
Sbjct: 343 WAYKK 347
Score = 103 bits (257), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 62/148 (41%), Positives = 84/148 (56%), Gaps = 16/148 (10%)
Query: 13 TVVAGILHDVVDDACESLGSIEEEFGDEVAKLVAGVSRLSYINQLLRRHRRINVNQGTLG 72
TV G LHDVV+D +L +IE +FG +V +V GV++L +
Sbjct: 70 TVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKLGKVE--------------YKS 115
Query: 73 HEE--ANDLRVMLLGMVDDPRVVLIKLADRLHNMRTIYALPPAKARAVAQETLLIWCSLA 130
HEE A + R ML+ M D RV+L+KLADRLHNMRT+ L K +++ET+ I+ LA
Sbjct: 116 HEEQLAENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLA 175
Query: 131 SRLGLWALKAELEDLCFAVLQPQIFRKM 158
RLG+ +K ELEDL F L F K+
Sbjct: 176 HRLGISRIKWELEDLAFRYLNETEFYKI 203
>pdb|3NR1|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
pdb|3NR1|B Chain B, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
Length = 178
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 51/112 (45%), Gaps = 18/112 (16%)
Query: 1 MLIPSSGKRAVDTVVAGILHDVVDDACESLGSIEEEFGDEVAKLVAGVSRLSYINQLLRR 60
+L +G + + A +LHD V+D +L +E FG +V +LV V+ + +L R
Sbjct: 41 ILTHEAGITDIVVLQAALLHDTVEDTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLER- 99
Query: 61 HRRINVNQGTLGHEEANDLRVMLLGMVDDPRVVLIKLADRLHNMRTIYALPP 112
+R+ V Q P L+KLAD+L+N+R + P
Sbjct: 100 -KRLQVEQAPHS----------------SPGAKLVKLADKLYNLRDLNRCTP 134
>pdb|3NQW|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
pdb|3NQW|B Chain B, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
Length = 179
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 50/114 (43%), Gaps = 20/114 (17%)
Query: 14 VVAGILHDVVDDACESLGSIEEEFGDEVAKLVAGVSRLSYINQLLRRHRRI-NVNQGTLG 72
++A +LHDVV+D S +E+ FG +V LV V+ + + R+ +I N + +
Sbjct: 56 LMAALLHDVVEDTDASFEDVEKLFGPDVCGLVREVTDDKSLEKQERKRLQIENAAKSSC- 114
Query: 73 HEEANDLRVMLLGMVDDPRVVLIKLADRLHNMRTIYALPPAKARAVAQETLLIW 126
R LIKLAD+L N+R + P ++ +W
Sbjct: 115 ------------------RAKLIKLADKLDNLRDLQVNTPTGWTQERRDQYFVW 150
>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 = 37.7 bits (86), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 9/56 (16%)
Query: 351 DYIVNPKPSGYQSLHTAVQGP----DGSAL---EVQIRTQKMHEYA--EHGLAAHW 397
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 = 33.9 bits (76), Expect = 0.35, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 656 RSGSTAADAAMKVGL--EGKLVLVNGQLVLPNTELKDGDIVEV 696
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 = 33.1 bits (74), Expect = 0.55, Method: Composition-based stats.
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 22/125 (17%)
Query: 282 LSSRLKSLYSIFSKMRRKDVGI----HKVYDARALRVVVGDKNGTLHGPAIQCCYSLLDI 337
++ R+K + SI K R+ + H + D LRV V + ++DI
Sbjct: 45 VTGRVKPIESIKEKXARRGITYATLEHDLQDIAGLRVXV---------QFVDDVKEVVDI 95
Query: 338 VHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQ-------GPDGSALEVQIRTQKMHEYA- 389
+H+ + DYI + K SGY+S H V+ G E+QIRT + +A
Sbjct: 96 LHKRQDXRIIQERDYITHRKASGYRSYHVVVEYTVDTINGAKTILAEIQIRTLAXNFWAT 155
Query: 390 -EHGL 393
EH L
Sbjct: 156 IEHSL 160
>pdb|1US4|A Chain A, Putative Glur0 Ligand Binding Core With L-Glutamate
Length = 314
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 275 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 318
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 = 3.5, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 275 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 318
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 = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 643 VIVCWPNGEIMRLRSGSTAADAAMK----VGLEGKLVLVNGQLVLPNTELKDGDIVEV 696
V+V P GEI RL G+TA D A +G VN +LV + L GD VEV
Sbjct: 3 VMVFTPKGEIKRLPQGATALDFAYSLHSDLGDHCIGAKVNHKLVPLSYVLNSGDQVEV 60
>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 = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 666 MKVGLEGKLVLVNGQLVLPNTELKDGDIVEV 696
+++ +E +V NGQ+V+ E+ DGDI+EV
Sbjct: 33 LEIPIETVVVKKNGQIVIDEEEIFDGDIIEV 63
>pdb|3CFW|A Chain A, L-selectin Lectin And Egf Domains
Length = 164
Score = 29.6 bits (65), Expect = 6.3, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 498 CWEAYARLYKKASDEWWCQPGHGDWCTCLEKYTL-CRDGMYHKQDQFGRLLPTFI 551
C + A L AS + W GHG+ + YT C G Y Q QF ++ P I
Sbjct: 109 CHKLKAALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVQVDPRLI 163
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 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,612,687
Number of Sequences: 62578
Number of extensions: 792971
Number of successful extensions: 1802
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1789
Number of HSP's gapped (non-prelim): 15
length of query: 698
length of database: 14,973,337
effective HSP length: 106
effective length of query: 592
effective length of database: 8,340,069
effective search space: 4937320848
effective search space used: 4937320848
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: 55 (25.8 bits)