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= 041295
(209 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 33 MDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92
M+V +++E + +R+ ++ I G P+ ++ S GV++D + +Y PY
Sbjct: 247 MEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGF 306
Query: 93 LMRT 96
L RT
Sbjct: 307 LART 310
>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
Length = 334
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 33 MDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92
M+V +++E + +R+ ++ I G P+ ++ S GV++D + +Y PY
Sbjct: 247 MEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGF 306
Query: 93 LMRT 96
L RT
Sbjct: 307 LART 310
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
Migration Motor
Length = 334
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 33 MDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92
M+V +++E + +R+ ++ I G P+ ++ S GV++D + +Y PY
Sbjct: 247 MEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGF 306
Query: 93 LMRT 96
L RT
Sbjct: 307 LART 310
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 33 MDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92
M+V +++E + +R+ ++ I G P+ ++ S GV++D + +Y PY
Sbjct: 247 MEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGF 306
Query: 93 LMRT 96
L RT
Sbjct: 307 LART 310
>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant
Length = 334
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 33 MDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92
M+V +++E + +R+ ++ I G P+ ++ S GV++D + +Y PY
Sbjct: 247 MEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGF 306
Query: 93 LMRT 96
L RT
Sbjct: 307 LART 310
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 33 MDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92
M+V +++E + +R+ ++ I G P+ ++ S GV++D + +Y PY
Sbjct: 247 MEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGF 306
Query: 93 LMRT 96
L RT
Sbjct: 307 LART 310
>pdb|2YWB|A Chain A, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
pdb|2YWB|B Chain B, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
pdb|2YWB|C Chain C, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
pdb|2YWB|D Chain D, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
Length = 503
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 166 EVEGKLENAGDNAKTADSCDRFKRALENQSELQDK 200
EVEG L G N D+ +RF +AL+ + ++K
Sbjct: 253 EVEGALRALGVNLLVVDAKERFLKALKGVEDPEEK 287
>pdb|2YWC|A Chain A, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
pdb|2YWC|B Chain B, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
pdb|2YWC|C Chain C, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
pdb|2YWC|D Chain D, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
Length = 503
Score = 26.9 bits (58), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 166 EVEGKLENAGDNAKTADSCDRFKRALENQSELQDK 200
EVEG L G N D+ +RF +AL+ + ++K
Sbjct: 253 EVEGALRALGVNLLVVDAKERFLKALKGVEDPEEK 287
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
0.315 0.133 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,592,868
Number of Sequences: 62578
Number of extensions: 276868
Number of successful extensions: 444
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 436
Number of HSP's gapped (non-prelim): 10
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)