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= 040497
(295 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|C Chain C, Taq Rna Polymerase-rifampicin Complex
pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1119
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 44/205 (21%), Positives = 84/205 (40%), Gaps = 33/205 (16%)
Query: 29 CVFMYLTPPEICNLARLNRAFRGAASSDSVWENKLPSNYQDLLDLMPPER--YLNLSKKE 86
V+M + + +A+ N G D + +++ + + ++ PE ++++S K+
Sbjct: 483 VVYMTASEEDRYTIAQANTPLEG----DRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQ 538
Query: 87 IFALLSRPVPF---DDGNKEVWLDRVTGRVCLSISTKA-MAITGIEDRRYWNWIPTEESR 142
+F+L + +PF DD N+ + + + I +A + +TG+E+R
Sbjct: 539 VFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEER------------ 586
Query: 143 FHVVAYLQQIWWFEVDGVVKFPLPADVYTVSFRLHLGRFAKRLGRRVCNFEHTHGWDIKP 202
VV + E DG V + D ++ R GR + RR +D +P
Sbjct: 587 --VVRDSLAALYAEEDGEV---VKVDGTRIAVRYEDGRLVEHPLRRYARSNQGTAFDQRP 641
Query: 203 -VRLELSTSDGQ-----QASSECYL 221
VR+ G AS E +L
Sbjct: 642 RVRVGQRVKKGDLLADGPASEEGFL 666
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1119
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 44/205 (21%), Positives = 84/205 (40%), Gaps = 33/205 (16%)
Query: 29 CVFMYLTPPEICNLARLNRAFRGAASSDSVWENKLPSNYQDLLDLMPPER--YLNLSKKE 86
V+M + + +A+ N G D + +++ + + ++ PE ++++S K+
Sbjct: 483 VVYMTASEEDRYTIAQANTPLEG----DRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQ 538
Query: 87 IFALLSRPVPF---DDGNKEVWLDRVTGRVCLSISTKA-MAITGIEDRRYWNWIPTEESR 142
+F+L + +PF DD N+ + + + I +A + +TG+E+R
Sbjct: 539 VFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEER------------ 586
Query: 143 FHVVAYLQQIWWFEVDGVVKFPLPADVYTVSFRLHLGRFAKRLGRRVCNFEHTHGWDIKP 202
VV + E DG V + D ++ R GR + RR +D +P
Sbjct: 587 --VVRDSLAALYAEEDGEV---VKVDGTRIAVRYEDGRLVEHPLRRYARSNQGTAFDQRP 641
Query: 203 -VRLELSTSDGQ-----QASSECYL 221
VR+ G AS E +L
Sbjct: 642 RVRVGQRVKKGDLLADGPASEEGFL 666
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1118
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 45/205 (21%), Positives = 84/205 (40%), Gaps = 34/205 (16%)
Query: 29 CVFMYLTPPEICNLARLNRAFRGAASSDSVWENKLPSNYQDLLDLMPPER--YLNLSKKE 86
V+M + + +A+ N G D + +++ + + ++ PE ++++S K+
Sbjct: 483 VVYMTASEEDRYTIAQANTPLEG----DRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQ 538
Query: 87 IFALLSRPVPF---DDGNKEVWLDRVTGRVCLSISTKA-MAITGIEDRRYWNWIPTEESR 142
+F+L + +PF DD N+ + + + I +A + +TG+E+R
Sbjct: 539 VFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEER------------ 586
Query: 143 FHVVAYLQQIWWFEVDGVVKFPLPADVYTVSFRLHLGRFAKRLGRRVCNFEHTHGWDIKP 202
VV + E DG V + D ++ R GR L RR +D +P
Sbjct: 587 --VVRDSLAALYAEEDGEV---VKVDGTRIAVRYEDGRLVHPL-RRYARSNQGTAFDQRP 640
Query: 203 -VRLELSTSDGQ-----QASSECYL 221
VR+ G AS E +L
Sbjct: 641 RVRVGQRVKKGDLLADGPASEEGFL 665
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 45/205 (21%), Positives = 84/205 (40%), Gaps = 34/205 (16%)
Query: 29 CVFMYLTPPEICNLARLNRAFRGAASSDSVWENKLPSNYQDLLDLMPPER--YLNLSKKE 86
V+M + + +A+ N G D + +++ + + ++ PE ++++S K+
Sbjct: 483 VVYMTASEEDRYTIAQANTPLEG----DRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQ 538
Query: 87 IFALLSRPVPF---DDGNKEVWLDRVTGRVCLSISTKA-MAITGIEDRRYWNWIPTEESR 142
+F+L + +PF DD N+ + + + I +A + +TG+E+R
Sbjct: 539 VFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEER------------ 586
Query: 143 FHVVAYLQQIWWFEVDGVVKFPLPADVYTVSFRLHLGRFAKRLGRRVCNFEHTHGWDIKP 202
VV + E DG V + D ++ R GR L RR +D +P
Sbjct: 587 --VVRDSLAALYAEEDGEV---VKVDGTRIAVRYEDGRLVHPL-RRYARSNQGTAFDQRP 640
Query: 203 -VRLELSTSDGQ-----QASSECYL 221
VR+ G AS E +L
Sbjct: 641 RVRVGQRVKKGDLLADGPASEEGFL 665
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
0.321 0.137 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,426,848
Number of Sequences: 62578
Number of extensions: 394368
Number of successful extensions: 600
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 600
Number of HSP's gapped (non-prelim): 4
length of query: 295
length of database: 14,973,337
effective HSP length: 98
effective length of query: 197
effective length of database: 8,840,693
effective search space: 1741616521
effective search space used: 1741616521
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)