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= 003497
(815 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 = 111 bits (278), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 72/181 (39%), Positives = 102/181 (56%), Gaps = 14/181 (7%)
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 ACESLGSIEEEFGDEVAKLVAGVSRL------SYINQLLRRHRRINVNQGT---LGHEEL 214
+L +IE +FG +V +V GV++L S+ QL HR++ + + +L
Sbjct: 83 TDITLDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQLAENHRKMLMAMSKDIRVILVKL 142
Query: 215 ADRLHNMRTIYALPPAKARAVAQETLLIWCSLASRLGLWALKAELEDLCFAVLQPQIFRK 274
ADRLHNMRT+ L K +++ET+ I+ LA RLG+ +K ELEDL F L F K
Sbjct: 143 ADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYK 202
Query: 275 M 275
+
Sbjct: 203 I 203
Score = 106 bits (265), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 52/125 (41%), Positives = 78/125 (62%), Gaps = 10/125 (8%)
Query: 394 GMEVTLSSRLKSLYSIFSKMRRKDVGIHKVYDARALRVVVGDKNGTLHGPAIQCCYSLLD 453
G+ + R K +YSI+ KMR K +++D A+R V+ ++ Y+++
Sbjct: 233 GLFGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSD---------VYAMVG 283
Query: 454 IVHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQGPDGSALEVQIRTQKMHEYAEHGLAAH 513
+H LW P+ G F DYI PK +GYQS+HT V GP G +E+QIRT++MH+ AE+G+AAH
Sbjct: 284 YIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGP-IEIQIRTKEMHQVAEYGVAAH 342
Query: 514 WLYKE 518
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 = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 44/134 (32%), Positives = 66/134 (49%), Gaps = 12/134 (8%)
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 VDDACESLGSIEEEFGDEVAKLVAGVSRLSYINQLLRRHRRINVNQGTLGHE-----ELA 215
V+D +L +E FG +V +LV V+ + +L R +R+ V Q +LA
Sbjct: 63 VEDTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLER--KRLQVEQAPHSSPGAKLVKLA 120
Query: 216 DRLHNMRTIYALPP 229
D+L+N+R + P
Sbjct: 121 DKLYNLRDLNRCTP 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 = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 68/145 (46%), Gaps = 12/145 (8%)
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-NVNQGTLGHE--ELADRL 218
+D S +E+ FG +V LV V+ + + R+ +I N + + + +LAD+L
Sbjct: 66 EDTDASFEDVEKLFGPDVCGLVREVTDDKSLEKQERKRLQIENAAKSSCRAKLIKLADKL 125
Query: 219 HNMRTIYALPPAKARAVAQETLLIW 243
N+R + P ++ +W
Sbjct: 126 DNLRDLQVNTPTGWTQERRDQYFVW 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 = 37.4 bits (85), Expect = 0.036, Method: Composition-based stats.
Identities = 24/52 (46%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 468 DYIVNPKPSGYQSLHTAVQGP----DGSAL---EVQIRTQKMHEYA--EHGL 510
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 = 0.26, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 773 RSGSTAADAAMKVGL--EGKLVLVNGQLVLPNTELKDGDIVEV 813
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 = 0.50, Method: Composition-based stats.
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 22/125 (17%)
Query: 399 LSSRLKSLYSIFSKMRRKDVGI----HKVYDARALRVVVGDKNGTLHGPAIQCCYSLLDI 454
++ R+K + SI K R+ + H + D LRV V + ++DI
Sbjct: 45 VTGRVKPIESIKEKXARRGITYATLEHDLQDIAGLRVXV---------QFVDDVKEVVDI 95
Query: 455 VHRLWIPIDGEFDDYIVNPKPSGYQSLHTAVQ-------GPDGSALEVQIRTQKMHEYA- 506
+H+ + DYI + K SGY+S H V+ G E+QIRT + +A
Sbjct: 96 LHKRQDXRIIQERDYITHRKASGYRSYHVVVEYTVDTINGAKTILAEIQIRTLAXNFWAT 155
Query: 507 -EHGL 510
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 = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 783 MKVGLEGKLVLVNGQLVLPNTELKDGDIVEV 813
+++ +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 = 3.6, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 392 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 435
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 = 4.0, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 392 IPGMEVTLSSRLKSLYSIFSKM----RRKDVGIHKVYDARALRVVVGD 435
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 = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 764 WPNGEIMRLRSGSTAADAAMKVGLE--GKLVLVNGQ----LVLPNTELKDGDIVEV 813
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 = 5.5, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 760 VIVCWPNGEIMRLRSGSTAADAAMK----VGLEGKLVLVNGQLVLPNTELKDGDIVEV 813
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 = 29.3 bits (64), Expect = 8.1, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 615 CWEAYARLYKKASDEWWCQPGHGDWCTCLEKYTL-CRDGMYHKQDQFGRLLPTFI 668
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 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,532,073
Number of Sequences: 62578
Number of extensions: 901032
Number of successful extensions: 1988
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1973
Number of HSP's gapped (non-prelim): 16
length of query: 815
length of database: 14,973,337
effective HSP length: 107
effective length of query: 708
effective length of database: 8,277,491
effective search space: 5860463628
effective search space used: 5860463628
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)