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= 024739
(263 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A3Q|A Chain A, The 2.15 Angstrom Resolution Crystal Structure Of
Staphylococcus Aureus Alanine Racemase
pdb|4A3Q|B Chain B, The 2.15 Angstrom Resolution Crystal Structure Of
Staphylococcus Aureus Alanine Racemase
Length = 382
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 203 PANMPLLSLNRRDGWMEIGIGEFFNENGDDGAVICRVCESEPTPK 247
P + LL + DG++ I G F N NG VI RVC + K
Sbjct: 274 PTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVK 318
>pdb|3OO2|A Chain A, 2.37 Angstrom Resolution Crystal Structure Of An Alanine
Racemase (Alr) From Staphylococcus Aureus Subsp. Aureus
Col
pdb|3OO2|B Chain B, 2.37 Angstrom Resolution Crystal Structure Of An Alanine
Racemase (Alr) From Staphylococcus Aureus Subsp. Aureus
Col
Length = 385
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 203 PANMPLLSLNRRDGWMEIGIGEFFNENGDDGAVICRVCESEPTPK 247
P + LL + DG++ I G F N NG VI RVC + K
Sbjct: 277 PTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVK 321
>pdb|1SI7|A Chain A, Structure Of E. Coli Trna Psi 13 Pseudouridine Synthase
Trud
Length = 369
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 61/161 (37%), Gaps = 19/161 (11%)
Query: 84 ILINNNTMSFALDHESGKKCYMVGARGLSITWGSSPQH-----WKWLSLPESRFPEVAEL 138
IL N F D + K + AR +S G +H W +P P+++
Sbjct: 68 ILKNGCNTRFVADALA--KFLKIHAREVSFA-GQKDKHAVTEQWLCARVPGKEMPDLSAF 124
Query: 139 KLVWCFEI-MARIETKI-LSSKTNYATYLVFKFVETREGFETRPIEFDV-----YFE--- 188
+L C + AR + K+ L + A LV + V R+ E R I+ V YF
Sbjct: 125 QLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQR 184
Query: 189 -GNDTHKMHSALLDPPANMPLLSLNRRDGWMEIGIGEFFNE 228
G + A N P+ N+R W+ FN+
Sbjct: 185 FGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQ 225
>pdb|1SB7|A Chain A, Crystal Structure Of The E.Coli Pseudouridine Synthase
Trud
pdb|1SB7|B Chain B, Crystal Structure Of The E.Coli Pseudouridine Synthase
Trud
Length = 368
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 61/161 (37%), Gaps = 19/161 (11%)
Query: 84 ILINNNTMSFALDHESGKKCYMVGARGLSITWGSSPQH-----WKWLSLPESRFPEVAEL 138
IL N F D + K + AR +S G +H W +P P+++
Sbjct: 67 ILKNGCNTRFVADALA--KFLKIHAREVSFA-GQKDKHAVTEQWLCARVPGKEXPDLSAF 123
Query: 139 KLVWCFEI-MARIETKI-LSSKTNYATYLVFKFVETREGFETRPIEFDV-----YFE--- 188
+L C + AR + K+ L + A LV + V R+ E R I+ V YF
Sbjct: 124 QLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQR 183
Query: 189 -GNDTHKMHSALLDPPANMPLLSLNRRDGWMEIGIGEFFNE 228
G + A N P+ N+R W+ FN+
Sbjct: 184 FGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQ 224
>pdb|1SZW|A Chain A, Crystal Structure Of E. Coli Trna Pseudouridine Synthase
Trud
pdb|1SZW|B Chain B, Crystal Structure Of E. Coli Trna Pseudouridine Synthase
Trud
Length = 379
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 61/161 (37%), Gaps = 19/161 (11%)
Query: 84 ILINNNTMSFALDHESGKKCYMVGARGLSITWGSSPQH-----WKWLSLPESRFPEVAEL 138
IL N F D + K + AR +S G +H W +P P+++
Sbjct: 70 ILKNGCNTRFVADALA--KFLKIHAREVSFA-GQKDKHAVTEQWLCARVPGKEXPDLSAF 126
Query: 139 KLVWCFEI-MARIETKI-LSSKTNYATYLVFKFVETREGFETRPIEFDV-----YFE--- 188
+L C + AR + K+ L + A LV + V R+ E R I+ V YF
Sbjct: 127 QLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQR 186
Query: 189 -GNDTHKMHSALLDPPANMPLLSLNRRDGWMEIGIGEFFNE 228
G + A N P+ N+R W+ FN+
Sbjct: 187 FGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQ 227
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 27.3 bits (59), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 112 SITWGSSPQHWKWLSLPES 130
SI+ G P+ WKW S+PE+
Sbjct: 3177 SISKGIVPKEWKWYSVPET 3195
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 112 SITWGSSPQHWKWLSLPES 130
SI+ G P+ WKW S+PE+
Sbjct: 3055 SISKGIVPKEWKWYSVPET 3073
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 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,920,499
Number of Sequences: 62578
Number of extensions: 311488
Number of successful extensions: 581
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 575
Number of HSP's gapped (non-prelim): 9
length of query: 263
length of database: 14,973,337
effective HSP length: 97
effective length of query: 166
effective length of database: 8,903,271
effective search space: 1477942986
effective search space used: 1477942986
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)