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= 025860
(247 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Q7M|A Chain A, Cobalamin-Dependent Methionine Synthase (Meth) From
Thermotoga Maritima (Oxidized, Monoclinic)
pdb|1Q7M|B Chain B, Cobalamin-Dependent Methionine Synthase (Meth) From
Thermotoga Maritima (Oxidized, Monoclinic)
pdb|1Q7Q|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From T.
Maritima (Oxidized, Orthorhombic)
pdb|1Q7Q|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From T.
Maritima (Oxidized, Orthorhombic)
pdb|1Q7Z|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex)
pdb|1Q7Z|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex)
pdb|1Q8J|A Chain A, Cobalamin-dependent Methionine Synthase (1-566) From
Thermotoga Maritima (cd2+, Hcy, Methyltetrahydrofolate
Complex)
pdb|1Q8J|B Chain B, Cobalamin-dependent Methionine Synthase (1-566) From
Thermotoga Maritima (cd2+, Hcy, Methyltetrahydrofolate
Complex)
pdb|3BOF|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+ And Homocysteine
pdb|3BOF|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+ And Homocysteine
pdb|3BOL|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+
pdb|3BOL|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+
Length = 566
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/188 (25%), Positives = 86/188 (45%), Gaps = 18/188 (9%)
Query: 63 GDAITVETLKDFHRRRVQVLVESAPDLIAFETIPN--KIXXXXXXXXXXXXNIKIPAWFS 120
G + E ++F R V+++VE D I FET + ++ ++ + A +
Sbjct: 117 GSTLFEEFYENF-RETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMT 175
Query: 121 FNSKDGVNVVSGDSLLECASIAESCKRVVSVGINCT-PPRFISGLILIIKKVTAKPILIY 179
F+ K G ++ D + E + ++GINC+ P I + + + T K +++
Sbjct: 176 FDEK-GRSLTGTDPANFAITFDEL--DIDALGINCSLGPEEILPIFQELSQYTDKFLVVE 232
Query: 180 PNSGEFYDADRKEWVQNTG----VSDEDFVSYVSKWCEVGASLVGGCCRTTPNTIKGIYR 235
PN+G K V+N + DF ++ + E+G ++ GGCC TTP +K +
Sbjct: 233 PNAG-------KPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRK 285
Query: 236 TLSNRSSV 243
L NR +
Sbjct: 286 VLGNRKPL 293
>pdb|1Q85|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex, Se-Met)
pdb|1Q85|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex, Se-Met)
pdb|1Q8A|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+:l-Hcy Complex, Se-Met)
pdb|1Q8A|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+:l-Hcy Complex, Se-Met)
Length = 566
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 47/188 (25%), Positives = 85/188 (45%), Gaps = 18/188 (9%)
Query: 63 GDAITVETLKDFHRRRVQVLVESAPDLIAFETIPN--KIXXXXXXXXXXXXNIKIPAWFS 120
G + E ++F R V++ VE D I FET + ++ ++ + A +
Sbjct: 117 GSTLFEEFYENF-RETVEIXVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHXT 175
Query: 121 FNSKDGVNVVSGDSLLECASIAESCKRVVSVGINCT-PPRFISGLILIIKKVTAKPILIY 179
F+ K G ++ D + E + ++GINC+ P I + + + T K +++
Sbjct: 176 FDEK-GRSLTGTDPANFAITFDEL--DIDALGINCSLGPEEILPIFQELSQYTDKFLVVE 232
Query: 180 PNSGEFYDADRKEWVQNTG----VSDEDFVSYVSKWCEVGASLVGGCCRTTPNTIKGIYR 235
PN+G K V+N + DF ++ + E+G ++ GGCC TTP +K +
Sbjct: 233 PNAG-------KPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRK 285
Query: 236 TLSNRSSV 243
L NR +
Sbjct: 286 VLGNRKPL 293
>pdb|4FXQ|A Chain A, Full-Length Certhrax Toxin From Bacillus Cereus In Complex
With Inhibitor P6
pdb|4FXQ|B Chain B, Full-Length Certhrax Toxin From Bacillus Cereus In Complex
With Inhibitor P6
pdb|4GF1|A Chain A, Crystal Structure Of Certhrax
pdb|4GF1|B Chain B, Crystal Structure Of Certhrax
Length = 460
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 6/38 (15%)
Query: 27 SVTDDRIPKHRPILVAASV--GSYGAYLADGSEYSGNY 62
S ++DR P IL+ ++ G +GAY+AD SEY G Y
Sbjct: 380 SYSNDRYP----ILLEITIPEGVHGAYIADMSEYPGQY 413
>pdb|4FK7|A Chain A, Crystal Structure Of Certhrax Catalytic Domain
Length = 229
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 6/38 (15%)
Query: 27 SVTDDRIPKHRPILVAASV--GSYGAYLADGSEYSGNY 62
S ++DR P IL+ ++ G +GAY+AD SEY G Y
Sbjct: 157 SYSNDRYP----ILLEITIPEGVHGAYIADMSEYPGQY 190
>pdb|3QO6|A Chain A, Crystal Structure Analysis Of The Plant Protease Deg1
pdb|3QO6|B Chain B, Crystal Structure Analysis Of The Plant Protease Deg1
pdb|3QO6|C Chain C, Crystal Structure Analysis Of The Plant Protease Deg1
Length = 348
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 63 GDAITVETLKDFHRRRVQVLVESAPD 88
GD +TVE L+ H+ ++ V +E PD
Sbjct: 310 GDEVTVEVLRGDHKEKISVTLEPKPD 335
>pdb|3IM9|A Chain A, Crystal Structure Of Mcat From Staphylococcus Aureus
Length = 316
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 14/81 (17%)
Query: 138 CASIAESCKRVVSVGINCTPPRFISGLILII-------KKVTAKPILIYPNSGEFYDADR 190
C S++ K + INC +SG +I K + AK ++ SG F+ +
Sbjct: 152 CKSLSSDDKIIEPANINCPGQIVVSGHKALIDELVEKGKSLGAKRVMPLAVSGPFHSSLM 211
Query: 191 KEWVQNTGVSDEDFVSYVSKW 211
K V +EDF SY++++
Sbjct: 212 K-------VIEEDFSSYINQF 225
>pdb|1UAS|A Chain A, Crystal Structure Of Rice Alpha-Galactosidase
Length = 362
Score = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 179 YPNSGEFYDADRKEWVQNTGVSDEDFVSYVSKWCEVGASLVGGC-CRTTPNTIKGI 233
Y G + D D E V N G+S+ ++ S+ S W A L+ GC R+ K I
Sbjct: 206 YAGPGGWNDPDMLE-VGNGGMSEAEYRSHFSIWALAKAPLLIGCDVRSMSQQTKNI 260
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
0.319 0.135 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,940,348
Number of Sequences: 62578
Number of extensions: 270261
Number of successful extensions: 681
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 675
Number of HSP's gapped (non-prelim): 7
length of query: 247
length of database: 14,973,337
effective HSP length: 96
effective length of query: 151
effective length of database: 8,965,849
effective search space: 1353843199
effective search space used: 1353843199
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)