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= 018876
(349 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 31.2 bits (69), Expect = 0.95, Method: Composition-based stats.
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 101 YNTLIDAYGRAKMFAEMELTLVKMLSEDCEPDVWTMNCTLRAFGNSGQ-IDTMEKCYEKF 159
YN ++ + R F E+ L + PD+ + L+ G Q T+E+C E+
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 160 QSAGIQ 165
G++
Sbjct: 228 SQEGLK 233
>pdb|3BKQ|X Chain X, Structure Of The P368g Mutant Of PmmPGM IN COMPLEX WITH
ITS SUBSTRATE
pdb|3C04|A Chain A, Structure Of The P368g Mutant Of PmmPGM FROM P. AERUGINOSA
Length = 463
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 3 GKCKQPEKAHELFQAMVDEGCDANTQSFTALLSAYGRSGLFDKAFSLLEHMKNTPDCQPD 62
G+ PE +L Q +VD GC + Y + + + ++ + P PD
Sbjct: 57 GRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGXHNP---PD 113
Query: 63 VNTYSILIKSCLKAFAFDKVQAL 85
N + I++ + A +++QAL
Sbjct: 114 YNGFKIVVAG--ETLANEQIQAL 134
>pdb|1K2Y|X Chain X, Crystal Structure Of Phosphomannomutase/phosphoglucomutase
S108a Mutant From P. Aeruginosa
Length = 463
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 3 GKCKQPEKAHELFQAMVDEGCDANTQSFTALLSAYGRSGLFDKAFSLLEHMKNTPDCQPD 62
G+ PE +L Q +VD GC + Y + + + ++ + P PD
Sbjct: 57 GRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGAHNP---PD 113
Query: 63 VNTYSILIKSCLKAFAFDKVQAL 85
N + I++ + A +++QAL
Sbjct: 114 YNGFKIVVAG--ETLANEQIQAL 134
>pdb|1P5D|X Chain X, Enzyme-Ligand Complex Of P. Aeruginosa PmmPGM
pdb|1P5G|X Chain X, Enzyme-Ligand Complex Of P. Aeruginosa PmmPGM
pdb|1PCJ|X Chain X, Enzyme-Ligand Complex Of P. Aeruginosa PmmPGM
pdb|1PCM|X Chain X, Enzyme-Ligand Complex Of P. Aeruginosa PmmPGM
Length = 463
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 3 GKCKQPEKAHELFQAMVDEGCDANTQSFTALLSAYGRSGLFDKAFSLLEHMKNTPDCQPD 62
G+ PE +L Q +VD GC + Y + + + ++ + P PD
Sbjct: 57 GRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGXHNP---PD 113
Query: 63 VNTYSILIKSCLKAFAFDKVQAL 85
N + I++ + A +++QAL
Sbjct: 114 YNGFKIVVAG--ETLANEQIQAL 134
>pdb|2H4L|X Chain X, Complex Of PmmPGM WITH RIBOSE 1-Phosphate
pdb|2H5A|X Chain X, Complex Of The Enzyme PmmPGM WITH XYLOSE 1-Phosphate
Length = 463
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 3 GKCKQPEKAHELFQAMVDEGCDANTQSFTALLSAYGRSGLFDKAFSLLEHMKNTPDCQPD 62
G+ PE +L Q +VD GC + Y + + + ++ + P PD
Sbjct: 57 GRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGXHNP---PD 113
Query: 63 VNTYSILIKSCLKAFAFDKVQAL 85
N + I++ + A +++QAL
Sbjct: 114 YNGFKIVVAG--ETLANEQIQAL 134
>pdb|2FKF|A Chain A, PhosphomannomutasePHOSPHOGLUCOMUTASE FROM PSEUDOMONAS
AERUGINOSA WITH Alpha-D-Glucose 1,6-Bisphosphate Bound
Length = 462
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 3 GKCKQPEKAHELFQAMVDEGCDANTQSFTALLSAYGRSGLFDKAFSLLEHMKNTPDCQPD 62
G+ PE +L Q +VD GC + Y + + + ++ + P PD
Sbjct: 56 GRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGXHNP---PD 112
Query: 63 VNTYSILIKSCLKAFAFDKVQAL 85
N + I++ + A +++QAL
Sbjct: 113 YNGFKIVVAG--ETLANEQIQAL 133
>pdb|2FKM|X Chain X, Pmm/pgm S108d Mutant With Alpha-d-glucose 1,6-bisphosphate
Bound
Length = 462
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 3 GKCKQPEKAHELFQAMVDEGCDANTQSFTALLSAYGRSGLFDKAFSLLEHMKNTPDCQPD 62
G+ PE +L Q +VD GC + Y + + + ++ + P PD
Sbjct: 56 GRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGDHNP---PD 112
Query: 63 VNTYSILIKSCLKAFAFDKVQAL 85
N + I++ + A +++QAL
Sbjct: 113 YNGFKIVVAG--ETLANEQIQAL 133
>pdb|2Z7X|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 520
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 29/117 (24%), Positives = 50/117 (42%), Gaps = 20/117 (17%)
Query: 206 YNIVIDAFGRAGDLKQMEYLFRLMRSERIKPSCVTLCSLVRAYGHAGKPEKLGSVLRFID 265
+ +V D FG Y++ + + IK V+ +V H P K+ L
Sbjct: 281 HQVVSDVFGFP-----QSYIYEIFSNMNIKNFTVSGTRMV----HMLCPSKISPFLHLDF 331
Query: 266 NSDIMLDTVFFNC--------LVDAYGRLK---CFAEMKGVLEVMQQRGCKPDKVTY 311
+++++ DTVF NC L+ +LK AEM ++ +QQ + V+Y
Sbjct: 332 SNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSY 388
>pdb|3RSM|A Chain A, Crystal Structure Of S108c Mutant Of PmmPGM
Length = 463
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 3 GKCKQPEKAHELFQAMVDEGCDANTQSFTALLSAYGRSGLFDKAFSLLEHMKNTPDCQPD 62
G+ PE +L Q +VD GC + Y + + + ++ + P PD
Sbjct: 57 GRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGCHNP---PD 113
Query: 63 VNTYSILIKSCLKAFAFDKVQAL 85
N + I++ + A +++QAL
Sbjct: 114 YNGFKIVVAG--ETLANEQIQAL 134
>pdb|2HYP|A Chain A, Crystal Structure Of Rv0805 D66a Mutant
Length = 280
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 227 RLMRSERIKPSCVTL----CSLV----RAYGHAGKPEKLGSVLRFIDNSDIMLDTVFFNC 278
RL +E +P V L L+ R YG ++LG +L ++ S + D + F
Sbjct: 5 RLRAAEHPRPDYVLLHISDTHLIGGDRRLYGAVDADDRLGELLEQLNQSGLRPDAIVFTG 64
Query: 279 LVDAYGRLKCFAEMKGVLE 297
+ A G + +++G++E
Sbjct: 65 DLAAKGEPAAYRKLRGLVE 83
>pdb|3CV2|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
Bacillis Anthracis Malate Synthase A: Comparison With
Isoform G And Implications For Structure Based Drug
Design
pdb|3CV2|B Chain B, Atomic Resolution Structures Of Escherichia Coli And
Bacillis Anthracis Malate Synthase A: Comparison With
Isoform G And Implications For Structure Based Drug
Design
Length = 532
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 12/51 (23%)
Query: 41 GLFDKAFSLLEHMKNTPDC-----------QPDVNTYS-ILIKSCLKAFAF 79
G +D FS ++ +KN PD +P +N YS +LIK+C K AF
Sbjct: 274 GRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSRLLIKTCHKRGAF 324
>pdb|3CUZ|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
Bacillis Anthracis Malate Synthase A: Comparison With
Isoform G And Implications For Structure Based Drug
Design
pdb|3CV1|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
Bacillis Anthracis Malate Synthase A: Comparison With
Isoform G And Implications For Structure Based Drug
Design
Length = 532
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 12/51 (23%)
Query: 41 GLFDKAFSLLEHMKNTPDC-----------QPDVNTYS-ILIKSCLKAFAF 79
G +D FS ++ +KN PD +P +N YS +LIK+C K AF
Sbjct: 274 GRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSRLLIKTCHKRGAF 324
>pdb|2J67|A Chain A, The Tir Domain Of Human Toll-Like Receptor 10 (Tlr10)
pdb|2J67|B Chain B, The Tir Domain Of Human Toll-Like Receptor 10 (Tlr10)
Length = 178
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 263 FIDNSD----IMLDTVFFNCLVDAYGRLKCFAEMKGVLEVMQQR 302
F +NSD I+L+ + F C+ Y +LK E K LE + R
Sbjct: 120 FHENSDHIILILLEPIPFYCIPTRYHKLKALLEKKAYLEWPKDR 163
>pdb|3HRA|A Chain A, Crystal Structure Of Ef0377 An Ankyrin Repeat Protein
Length = 201
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 57/126 (45%), Gaps = 21/126 (16%)
Query: 13 ELFQAMVDEGCDANTQSFTA-----LLSAYGRSGLFDKAFSLLEHMKNTPDCQPDVNTY- 66
E+ +A++D G D N Q+ + A GR+ + A+ +L+H PD+N +
Sbjct: 53 EIAKALIDRGADINLQNSISDSPYLYAGAQGRTEIL--AY-MLKH------ATPDLNKHN 103
Query: 67 ----SILIKSCLKAFAFDKVQALLSDMSTQGIRPNTVTYNTLIDAYGRAKMFAEMELTLV 122
+ LI + K D V+ LL D N Y LI+A G + ++ +V
Sbjct: 104 RYGGNALIPAAEKGH-IDNVKLLLEDGREDIDFQNDFGYTALIEAVG-LREGNQLYQDIV 161
Query: 123 KMLSED 128
K+L E+
Sbjct: 162 KLLMEN 167
>pdb|1MDC|A Chain A, Crystallization, Structure Determination And Least-Squares
Refinement To 1.75 Angstroms Resolution Of The
Fatty-Acid-Binding Protein Isolated From Manduca Sexta L
Length = 132
Score = 28.1 bits (61), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 80 DKVQALLSDMSTQGIRPNTVTYNTLIDAYGRAKMFA 115
DK+QAL+SD TQ + N +Y+ G AK +
Sbjct: 28 DKIQALVSDKPTQKMEANGDSYSNTSTGGGGAKTVS 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
0.323 0.135 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,102,168
Number of Sequences: 62578
Number of extensions: 390626
Number of successful extensions: 916
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 912
Number of HSP's gapped (non-prelim): 18
length of query: 349
length of database: 14,973,337
effective HSP length: 100
effective length of query: 249
effective length of database: 8,715,537
effective search space: 2170168713
effective search space used: 2170168713
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)