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= 005604
(688 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A4L|A Chain A, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4L|B Chain B, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4M|A Chain A, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4M|B Chain B, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4N|A Chain A, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4N|B Chain B, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3AM1|A Chain A, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Anticodon-StemLOOP TRUNCATED TRNA(SEC)
Length = 260
Score = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 40/171 (23%), Positives = 80/171 (46%), Gaps = 30/171 (17%)
Query: 263 MKDCEVMMMVGLPASGKTTWAEKWVKDHPEKRY--ILLGTNLILEQMKVPGLLRKHNYSE 320
M D ++++ GLP GK+T+++ K + I+LG++LI E V + E
Sbjct: 1 MGDIMLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPV--------WKE 52
Query: 321 RFQCLMGRAN-AIFDVLLSRASRTPRNF--IIDQTNVFKSARKRKLRLFVNFRKIAVVVF 377
+++ + ++ + D L +N+ I+D TN + S R+ + + + K +++
Sbjct: 53 KYEEFIKKSTYRLIDSAL-------KNYWVIVDDTNYYNSMRRDLINIAKKYNKNYAIIY 105
Query: 378 PKPE-DLKIRSVKRFKEMGKEVPADAVNNMLANYVLPVNKDTPGSDELFDQ 427
K D+ IR R E G+++P + + M + D PG +D+
Sbjct: 106 LKASLDVLIR---RNIERGEKIPNEVIKKMYEKF------DEPGKKYKWDE 147
>pdb|3ADB|A Chain A, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Selenocysteine Trna And Amppnp (Crystal Type 1)
pdb|3ADB|B Chain B, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Selenocysteine Trna And Amppnp (Crystal Type 1)
pdb|3ADC|A Chain A, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Selenocysteine Trna And Amppnp (Crystal Type 2)
pdb|3ADC|B Chain B, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Selenocysteine Trna And Amppnp (Crystal Type 2)
pdb|3ADD|A Chain A, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Selenocysteine Trna And Amppnp (Crystal Type 3)
pdb|3ADD|B Chain B, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Selenocysteine Trna And Amppnp (Crystal Type 3)
Length = 259
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 37/166 (22%), Positives = 77/166 (46%), Gaps = 30/166 (18%)
Query: 268 VMMMVGLPASGKTTWAEKWVKDHPEKRY--ILLGTNLILEQMKVPGLLRKHNYSERFQCL 325
++++ GLP GK+T+++ K + I+LG++LI E V + E+++
Sbjct: 13 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPV--------WKEKYEEF 64
Query: 326 MGRANA-IFDVLLSRASRTPRNF--IIDQTNVFKSARKRKLRLFVNFRKIAVVVFPKPE- 381
+ ++ + D L +N+ I+D TN + S R+ + + + K +++ K
Sbjct: 65 IKKSTYRLIDSAL-------KNYWVIVDDTNYYNSXRRDLINIAKKYNKNYAIIYLKASL 117
Query: 382 DLKIRSVKRFKEMGKEVPADAVNNMLANYVLPVNKDTPGSDELFDQ 427
D+ IR R E G+++P + + + D PG +D+
Sbjct: 118 DVLIR---RNIERGEKIPNEVIKKXYEKF------DEPGKKYKWDE 154
>pdb|4GP6|A Chain A, Polynucleotide Kinase
pdb|4GP6|B Chain B, Polynucleotide Kinase
Length = 171
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 57/120 (47%), Gaps = 15/120 (12%)
Query: 265 DCEVMMMVGLPASGKTTWAEKWVKDHPEKRYILLGTNLILEQMKVPGLLRKHNYSERFQC 324
+ +++++G SGK+T+A+K K T +I GL+ E Q
Sbjct: 8 ELSLVVLIGSSGSGKSTFAKKHFKP----------TEVISSDF-CRGLVSD---DENDQT 53
Query: 325 LMGRANAIFDVLLSRASRTPRNFIIDQTNVFKSARKRKLRLFVNFRKIAV-VVFPKPEDL 383
+ G A + ++S+ + + ++D TNV +SARK + + ++ V VVF PE +
Sbjct: 54 VTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEKV 113
>pdb|1LTQ|A Chain A, Crystal Structure Of T4 Polynucleotide Kinase
pdb|1RC8|A Chain A, T4 Polynucleotide Kinase Bound To 5'-Gtcac-3' Ssdna
pdb|1RPZ|A Chain A, T4 Polynucleotide Kinase Bound To 5'-Tgcac-3' Ssdna
pdb|1RRC|A Chain A, T4 Polynucleotide Kinase Bound To 5'-Gtc-3' Ssdna
Length = 301
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 267 EVMMMVGLPASGKTTWAEKWVKDHP 291
++++ +G P SGK+TWA +++ +P
Sbjct: 3 KIILTIGCPGSGKSTWAREFIAKNP 27
>pdb|1LY1|A Chain A, Structure And Mechanism Of T4 Polynucleotide Kinase
Length = 181
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 267 EVMMMVGLPASGKTTWAEKWVKDHP 291
++++ +G P SGK+TWA +++ +P
Sbjct: 3 KIILTIGCPGSGKSTWAREFIAKNP 27
>pdb|2IA5|A Chain A, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|B Chain B, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|C Chain C, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|D Chain D, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|E Chain E, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|F Chain F, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|G Chain G, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|H Chain H, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|I Chain I, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|J Chain J, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|K Chain K, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium.
pdb|2IA5|L Chain L, T4 Polynucleotide KinasePHOSPHATASE WITH BOUND SULFATE AND
Magnesium
Length = 301
Score = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 267 EVMMMVGLPASGKTTWAEKWVKDHP 291
++++ +G P SGK+TWA +++ +P
Sbjct: 3 KIILTIGCPGSGKSTWAREFIAKNP 27
>pdb|2EFC|A Chain A, Ara7-GdpATVPS9A
pdb|2EFC|C Chain C, Ara7-GdpATVPS9A
pdb|2EFD|A Chain A, Ara7ATVPS9A
pdb|2EFD|C Chain C, Ara7ATVPS9A
pdb|2EFE|A Chain A, Ara7-Gdpnh2ATVPS9A
pdb|2EFE|C Chain C, Ara7-Gdpnh2ATVPS9A
pdb|4G01|A Chain A, Ara7-gdp-ca2+/vps9a
Length = 267
Score = 29.3 bits (64), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 403 VNNMLANYVLPVNKDTPGSDELFDQVMFVELDREEAQRH 441
+NN+L N + N++ PG+DE +++V + Q H
Sbjct: 168 INNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLH 206
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
0.316 0.134 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,015,960
Number of Sequences: 62578
Number of extensions: 875171
Number of successful extensions: 1926
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1916
Number of HSP's gapped (non-prelim): 13
length of query: 688
length of database: 14,973,337
effective HSP length: 105
effective length of query: 583
effective length of database: 8,402,647
effective search space: 4898743201
effective search space used: 4898743201
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)