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= 003255
(836 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 = 128 bits (322), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 80/195 (41%), Positives = 109/195 (55%), Gaps = 21/195 (10%)
Query: 104 VQKAIAFAKRAHHGQFRKTGDPYLTHCIHTGRILAMLIPSSGKRAVDTVVAGILHDVVDD 163
V+KA+ +A AH Q RK+G+PY+ H I ILA L + TV G LHDVV+D
Sbjct: 28 VKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAV-----TVACGFLHDVVED 82
Query: 164 ACESLGSIEEEFGDEVAKLVAGVSRLSYINQLLRRHRRINVNQGTLGHEE--ANDLRVML 221
+L +IE +FG +V +V GV++L + HEE A + R ML
Sbjct: 83 TDITLDNIEFDFGKDVRDIVDGVTKLGKVE--------------YKSHEEQLAENHRKML 128
Query: 222 LGMVDDPRVVLIKLADRLHNMRTIYALPPAKARAVAQETLLIWCSLASRLGLWALKAELE 281
+ M D RV+L+KLADRLHNMRT+ L K +++ET+ I+ LA RLG+ +K ELE
Sbjct: 129 MAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELE 188
Query: 282 DLCFAVLQPQIFRKM 296
DL F L F K+
Sbjct: 189 DLAFRYLNETEFYKI 203
Score = 106 bits (265), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 52/125 (41%), Positives = 78/125 (62%), Gaps = 10/125 (8%)
Query: 415 GMEVTLSSRLKSLYSIFSKMRRKDVGIHKVYDARALRVVVGDKNGTLHGPAIQCCYSLLD 474
G+ + R K +YSI+ KMR K +++D A+R V+ ++ Y+++
Sbjct: 233 GLFGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSD---------VYAMVG 283
Query: 475 IVHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQGPDGSALEVQIRTQKMHEYAEHGLAAH 534
+H LW P+ G F DYI PK +GYQS+HT V GP G +E+QIRT++MH+ AE+G+AAH
Sbjct: 284 YIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGP-IEIQIRTKEMHQVAEYGVAAH 342
Query: 535 WLYKE 539
W YK+
Sbjct: 343 WAYKK 347
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 47/150 (31%), Positives = 69/150 (46%), Gaps = 23/150 (15%)
Query: 103 QVQKAIAFAKRAHHGQFRK--TGDPYLTHCIHTGRILAMLIPSSGKRAVDTVVAGILHDV 160
Q+ +A FA R H Q RK G PY+ H I RIL +G + + A +LHD
Sbjct: 6 QLLEAADFAARKHRQQRRKDPEGTPYINHPIGVARILTH---EAGITDIVVLQAALLHDT 62
Query: 161 VDDACESLGSIEEEFGDEVAKLVAGVSRLSYINQLLRRHRRINVNQGTLGHEEANDLRVM 220
V+D +L +E FG +V +LV V+ + +L R +R+ V Q
Sbjct: 63 VEDTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLER--KRLQVEQAPHS---------- 110
Query: 221 LLGMVDDPRVVLIKLADRLHNMRTIYALPP 250
P L+KLAD+L+N+R + P
Sbjct: 111 ------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 = 49.7 bits (117), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 43/164 (26%), Positives = 70/164 (42%), Gaps = 29/164 (17%)
Query: 106 KAIAFAKRAHHGQFRKTGD--PYLTHCIHTGRILAM--LIPSSGKRAVDTVVAGILHDVV 161
+ + +A H Q RK PY+ H I+ IL++ I G ++A +LHDVV
Sbjct: 11 ECLQYAAFKHRQQRRKDPQETPYVNHVINVSTILSVEACITDEG-----VLMAALLHDVV 65
Query: 162 DDACESLGSIEEEFGDEVAKLVAGVSRLSYINQLLRRHRRI-NVNQGTLGHEEANDLRVM 220
+D S +E+ FG +V LV V+ + + R+ +I N + +
Sbjct: 66 EDTDASFEDVEKLFGPDVCGLVREVTDDKSLEKQERKRLQIENAAKSSC----------- 114
Query: 221 LLGMVDDPRVVLIKLADRLHNMRTIYALPPAKARAVAQETLLIW 264
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 = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 489 DYIVNPKPSGYQSLHTAVQGP----DGSAL---EVQIRTQKMHEYA--EHGL 531
DYI N KPSGY+S H V+ P G + E+QIRT M+ +A EH L
Sbjct: 138 DYINNLKPSGYRSYHVIVEYPVDTISGQRIIMAEIQIRTLAMNFWATIEHSL 189
>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 = 0.30, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 794 RSGSTAADAAMKVGL--EGKLVLVNGQLVLPNTELKDGDIVEV 834
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 = 33.5 bits (75), Expect = 0.51, Method: Composition-based stats.
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 22/125 (17%)
Query: 420 LSSRLKSLYSIFSKMRRKDVGI----HKVYDARALRVVVGDKNGTLHGPAIQCCYSLLDI 475
++ R+K + SI K R+ + H + D LRV V + ++DI
Sbjct: 45 VTGRVKPIESIKEKXARRGITYATLEHDLQDIAGLRVXV---------QFVDDVKEVVDI 95
Query: 476 VHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQ-------GPDGSALEVQIRTQKMHEYA- 527
+H+ + DYI + K SGY+S H V+ G E+QIRT + +A
Sbjct: 96 LHKRQDXRIIQERDYITHRKASGYRSYHVVVEYTVDTINGAKTILAEIQIRTLAXNFWAT 155
Query: 528 -EHGL 531
EH L
Sbjct: 156 IEHSL 160
>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: 804 MKVGLEGKLVLVNGQLVLPNTELKDGDIVEV 834
+++ +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 = 3.8, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 413 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 456
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 = 4.2, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 413 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 456
IP E +++L +++ ++ RKD GI V D + RVVVGD
Sbjct: 91 IPAFEGKPVKTIRALAALYPEVVHVVARKDAGIRTVADLKGKRVVVGD 138
>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 = 5.1, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 785 WPNGEIMRLRSGSTAADAAMKVGLE--GKLVLVNGQ----LVLPNTELKDGDIVEV 834
W NGE R G T + + G+E G VL+N + L +P+ L+DGD+VEV
Sbjct: 3 WLNGE-PRPLEGKTLKEVLEEXGVELKGVAVLLNEEAFLGLEVPDRPLRDGDVVEV 57
>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 = 5.1, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 781 VIVCWPNGEIMRLRSGSTAADAAMK----VGLEGKLVLVNGQLVLPNTELKDGDIVEV 834
V+V P GEI RL G+TA D A +G VN +LV + L GD VEV
Sbjct: 3 VMVFTPKGEIKRLPQGATALDFAYSLHSDLGDHCIGAKVNHKLVPLSYVLNSGDQVEV 60
>pdb|3CFW|A Chain A, L-selectin Lectin And Egf Domains
Length = 164
Score = 29.6 bits (65), Expect = 7.7, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 636 CWEAYARLYKKASDEWWCQPGHGDWCTCLEKYTL-CRDGMYHKQDQFGRLLPTFI 689
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
0.320 0.135 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,049,526
Number of Sequences: 62578
Number of extensions: 921169
Number of successful extensions: 2040
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: 2025
Number of HSP's gapped (non-prelim): 15
length of query: 836
length of database: 14,973,337
effective HSP length: 107
effective length of query: 729
effective length of database: 8,277,491
effective search space: 6034290939
effective search space used: 6034290939
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)