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= 007823
(588 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IKL|A Chain A, Crystal Structure Of Pol Gb Delta-I4.
pdb|3IKL|B Chain B, Crystal Structure Of Pol Gb Delta-I4
Length = 459
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 5 LETHQKQLEELQDKYDCQVRQCSDLTTKLELTESNLDQTIKLLNNTEEQLKKCQYALKEK 64
LET Q LE+L KYD + S L T L +TE+ L+ + L + + +K+ + K K
Sbjct: 386 LETMQSSLEQLYSKYD----EMSILFTVL-VTETTLENGLIHLRSRDTTMKEMMHISKLK 440
Query: 65 DFIISEQKKAENA 77
DF+I A+N
Sbjct: 441 DFLIKYISSAKNV 453
>pdb|2G4C|A Chain A, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|B Chain B, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|C Chain C, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|D Chain D, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
Length = 474
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 5 LETHQKQLEELQDKYDCQVRQCSDLTTKLELTESNLDQTIKLLNNTEEQLKKCQYALKEK 64
LET Q LE+L KYD + S L T L +TE+ L+ + L + + +K+ + K K
Sbjct: 407 LETMQSSLEQLYSKYD----EMSILFTVL-VTETTLENGLIHLRSRDTTMKEMMHISKLK 461
Query: 65 DFIISEQKKAENA 77
DF+I A+N
Sbjct: 462 DFLIKYISSAKNV 474
>pdb|3IKM|B Chain B, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|C Chain C, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|E Chain E, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|F Chain F, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
Length = 427
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 5 LETHQKQLEELQDKYDCQVRQCSDLTTKLELTESNLDQTIKLLNNTEEQLKKCQYALKEK 64
LET Q LE+L KYD + S L T L +TE+ L+ + L + + +K+ + K K
Sbjct: 360 LETMQSSLEQLYSKYD----EMSILFTVL-VTETTLENGLIHLRSRDTTMKEMMHISKLK 414
Query: 65 DFIISEQKKAENA 77
DF+I A+N
Sbjct: 415 DFLIKYISSAKNV 427
>pdb|2IWC|A Chain A, Benzylpenicilloyl-Acylated Mecr1 Extracellular
Antibiotic- Sensor Domain
Length = 255
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 24 RQCSDLTTKLELTESNLDQTIKLLNNTEEQLKKCQYALKE 63
R + T K+ L DQ + LN+TE+Q K QY KE
Sbjct: 56 RYSPNXTYKIYLALMAFDQNLLSLNHTEQQWDKHQYPFKE 95
>pdb|2IWD|A Chain A, Oxacilloyl-Acylated Mecr1 Extracellular
Antibiotic-Sensor Domain
Length = 246
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 24 RQCSDLTTKLELTESNLDQTIKLLNNTEEQLKKCQYALKE 63
R + T K+ L DQ + LN+TE+Q K QY KE
Sbjct: 47 RYSPNXTYKIYLALMAFDQNLLSLNHTEQQWDKHQYPFKE 86
>pdb|2IWB|A Chain A, Mecr1 Unbound Extracellular Antibiotic-Sensor Domain
Length = 246
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 24 RQCSDLTTKLELTESNLDQTIKLLNNTEEQLKKCQYALKE 63
R + T K+ L DQ + LN+TE+Q K QY KE
Sbjct: 47 RYSPNSTYKIYLALMAFDQNLLSLNHTEQQWDKHQYPFKE 86
>pdb|3TNF|B Chain B, Lida From Legionella In Complex With Active Rab8a
Length = 384
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 25/43 (58%)
Query: 10 KQLEELQDKYDCQVRQCSDLTTKLELTESNLDQTIKLLNNTEE 52
K+ EEL+ K D RQ DL K + E NL+ KLL ++EE
Sbjct: 18 KKGEELEKKLDKLERQGKDLEDKYKTYEENLEGFEKLLTDSEE 60
>pdb|3TKL|B Chain B, Crystal Structure Of The Gtp-Bound Rab1a In Complex With
The Coiled- Coil Domain Of Lida From Legionella
Pneumophila
Length = 267
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 25/43 (58%)
Query: 10 KQLEELQDKYDCQVRQCSDLTTKLELTESNLDQTIKLLNNTEE 52
K+ EEL+ K D RQ DL K + E NL+ KLL ++EE
Sbjct: 35 KKGEELEKKLDKLERQGKDLEDKYKTYEENLEGFEKLLTDSEE 77
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
0.312 0.124 0.336
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,189,506
Number of Sequences: 62578
Number of extensions: 504505
Number of successful extensions: 1189
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 1179
Number of HSP's gapped (non-prelim): 36
length of query: 588
length of database: 14,973,337
effective HSP length: 104
effective length of query: 484
effective length of database: 8,465,225
effective search space: 4097168900
effective search space used: 4097168900
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)