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= 023487
(281 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PMZ|N Chain N, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Y Chain Y, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|N Chain N, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|W Chain W, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 66
Score = 29.3 bits (64), Expect = 2.5, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 117 PALCFSCGYFAYDQWDMLQYRLYSGLIPGILVHHL 151
P CF+CG D+W R+ +G PG ++ L
Sbjct: 4 PIRCFTCGSLIADKWQSFITRVNAGENPGKVLDDL 38
>pdb|2WAQ|N Chain N, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|N Chain N, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|O Chain O, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|N Chain N, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|O Chain O, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|N Chain N, Rnap At 3.2ang
pdb|4B1O|N Chain N, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|O Chain O, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 66
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 117 PALCFSCGYFAYDQWDMLQYRLYSGLIPGILVHHL 151
P CF+CG D+W R+ +G PG ++ L
Sbjct: 4 PIRCFTCGSLIADKWQPFITRVNAGENPGKVLDDL 38
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 236 EKGIELPLALFGMAGMNLLNISLG----IDLFNAFKREKNPQQTSY 277
E G ++ L F AG+ LN++LG I++ +A K P T Y
Sbjct: 77 EPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIY 122
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 236 EKGIELPLALFGMAGMNLLNISLG----IDLFNAFKREKNPQQTSY 277
E G ++ L F AG+ LN++LG I++ +A K P T Y
Sbjct: 80 EPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIY 125
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 236 EKGIELPLALFGMAGMNLLNISLG----IDLFNAFKREKNPQQTSY 277
E G ++ L F AG+ LN++LG I++ +A K P T Y
Sbjct: 80 EPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIY 125
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 27.3 bits (59), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 236 EKGIELPLALFGMAGMNLLNISLG----IDLFNAFKREKNPQQTSY 277
E G ++ L F AG+ LN++LG I++ +A K P T Y
Sbjct: 80 EPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIY 125
>pdb|3ZXK|A Chain A, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
pdb|3ZXK|B Chain B, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
Length = 542
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 93 WLRNGLNGMFEHSELVGSAWLWAYPALCFSCGYFA 127
W G N + + E+ SAW W + A +C Y A
Sbjct: 110 WTSPGGNALANNGEVPPSAWNWQHTATIDNCYYDA 144
>pdb|3ZXJ|A Chain A, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
pdb|3ZXJ|B Chain B, Engineering The Active Site Of A Gh43 Glycoside Hydrolase
Generates A Biotechnologically Significant Enzyme That
Displays Both Endo-Xylanase And Exo-Arabinofuranosidase
Activity
Length = 542
Score = 27.3 bits (59), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 93 WLRNGLNGMFEHSELVGSAWLWAYPALCFSCGYFA 127
W G N + + E+ SAW W + A +C Y A
Sbjct: 110 WTSPGGNALANNGEVPPSAWNWQHTATIDNCYYDA 144
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
0.331 0.142 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,516,351
Number of Sequences: 62578
Number of extensions: 264874
Number of successful extensions: 372
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 368
Number of HSP's gapped (non-prelim): 8
length of query: 281
length of database: 14,973,337
effective HSP length: 98
effective length of query: 183
effective length of database: 8,840,693
effective search space: 1617846819
effective search space used: 1617846819
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (24.3 bits)