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= 030813
(171 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OXW|A Chain A, The Crystal Structure Of Semet Patatin
pdb|1OXW|B Chain B, The Crystal Structure Of Semet Patatin
pdb|1OXW|C Chain C, The Crystal Structure Of Semet Patatin
Length = 373
Score = 135 bits (341), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 72/160 (45%), Positives = 97/160 (60%), Gaps = 15/160 (9%)
Query: 9 GKKITVLSXXXXXXXXXXXXXXLAFLESKLQELDGPS-ARIADYFDVVAGTSTGGLVTTM 67
G+ +TVLS L FLE +LQE D + AR+ADYFDV+ GTSTGGL+T
Sbjct: 13 GEXVTVLSIDGGGIRGIIPATILEFLEGQLQEXDNNADARLADYFDVIGGTSTGGLLTAX 72
Query: 68 LTAPNKEGGPFIAAKDINNFYLEHGPKIFPQISRSNFSESIASSIDKRLLGPKYDGKYLR 127
++ PN+ PF AAK+I FY EHGP+IF + ++LGPKYDGKYL
Sbjct: 73 ISTPNENNRPFAAAKEIVPFYFEHGPQIF--------------NPSGQILGPKYDGKYLX 118
Query: 128 ALVNELLGDVTVKETLTNVVIPTFDIKLLQPVIFSTTDVC 167
++ E LG+ V + LT VVI +FDIK +PVIF+ +++
Sbjct: 119 QVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLA 158
>pdb|3VDI|A Chain A, Structure Of The Fmo Protein From Pelodictyon Phaeum
Length = 367
Score = 27.7 bits (60), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 74 EGGPFIAAKDINNFYLEHGPKIFPQISRSNFSESIASSID 113
EGG I+ +NNF +E G K +SR FS + + +D
Sbjct: 196 EGGQRISPIQVNNFGVESGEKGPVGVSRWKFSHAGSGIVD 235
>pdb|3P9D|E Chain E, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9D|M Chain M, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|EE Chain e, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|MM Chain m, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|4D8Q|E Chain E, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8Q|M Chain M, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|EE Chain e, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|MM Chain m, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
Length = 562
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 64 VTTMLTAPNKEGGPFIAAKDINNFYLEHGPKIFPQISRSNFSESIASSIDKRLLGPK 120
++ + A ++ G PFI KD N +HG + + S + S+AS I K LGP+
Sbjct: 15 LSNAIVAQDEMGRPFIIVKDQGNKKRQHG--LEAKKSHILAARSVASII-KTSLGPR 68
>pdb|2YK4|A Chain A, Structure Of Neisseria Los-Specific Sialyltransferase
(Nst)
Length = 327
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 53 DVVAGTSTGGLVTTMLTAPNKEGGPF--IAAKDINNFYLEHGPK 94
++ AG TGG V +L +P+KE AAK+ N Y+ P+
Sbjct: 192 ELKAGDETGGTVRILLGSPDKEXKEISEKAAKNFNIQYVAPHPR 235
>pdb|2YK5|A Chain A, Structure Of Neisseria Los-Specific Sialyltransferase
(Nst), In Complex With Cmp
Length = 326
Score = 26.9 bits (58), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 53 DVVAGTSTGGLVTTMLTAPNKEGGPF--IAAKDINNFYLEHGPK 94
++ AG TGG V +L +P+KE AAK+ N Y+ P+
Sbjct: 191 ELKAGDETGGTVRILLGSPDKEXKEISEKAAKNFNIQYVAPHPR 234
>pdb|2I62|A Chain A, Mouse Nicotinamide N-methyltransferase
pdb|2I62|B Chain B, Mouse Nicotinamide N-methyltransferase
pdb|2I62|C Chain C, Mouse Nicotinamide N-methyltransferase
pdb|2I62|D Chain D, Mouse Nicotinamide N-methyltransferase
Length = 265
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 115 RLLGPKYDGKYLRALVNELLGDVTVKETLTNVVIPTFDIKL 155
R+ GP+ + K RA+ L DVT + L V +P D L
Sbjct: 122 RMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLL 162
>pdb|1KSA|A Chain A, Crystal Structure Of The Bacteriochlorophyll A Protein
From Chlorobium Tepidum
pdb|1KSA|B Chain B, Crystal Structure Of The Bacteriochlorophyll A Protein
From Chlorobium Tepidum
pdb|3BSD|A Chain A, Light Harvesting Protein From Rc Of Chlorobium Tepidum
Length = 366
Score = 26.6 bits (57), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 63 LVTTMLTAPNKEGGPFIAAKDINNFYLEHGPKIFPQISRSNFSESIASSID 113
+ TA N EGG I+ ++N E GPK +SR FS + +D
Sbjct: 185 FIGPAFTALN-EGGQRISRIEVNGLNTESGPKGPVGVSRWRFSHGGSGMVD 234
>pdb|3ENI|A Chain A, Crystal Structure Of The Fenna-Matthews-Olson Protein From
Chlorobaculum Tepidum
pdb|3ENI|C Chain C, Crystal Structure Of The Fenna-Matthews-Olson Protein From
Chlorobaculum Tepidum
Length = 365
Score = 26.6 bits (57), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 63 LVTTMLTAPNKEGGPFIAAKDINNFYLEHGPKIFPQISRSNFSESIASSID 113
+ TA N EGG I+ ++N E GPK +SR FS + +D
Sbjct: 184 FIGPAFTALN-EGGQRISRIEVNGLNTESGPKGPVGVSRWRFSHGGSGMVD 233
>pdb|1CPY|A Chain A, Site-Directed Mutagenesis On (Serine) Carboxypeptidase Y
From Yeast. The Significance Of Thr 60 And Met 398 In
Hydrolysis And Aminolysis Reactions
Length = 421
Score = 26.6 bits (57), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 9/69 (13%)
Query: 80 AAKDINNFYLEHGPKIFPQISRSNFSESIASSIDKRLLGPKYDGKYLRALVNELLGDVTV 139
A KD+ NF ++ F E + D + G Y G Y+ +E+L
Sbjct: 115 AGKDVYNFL---------ELFFDQFPEYVNKGQDFHIAGASYAGHYIPVFASEILSHKDR 165
Query: 140 KETLTNVVI 148
LT+V+I
Sbjct: 166 NFNLTSVLI 174
>pdb|1WPX|A Chain A, Crystal Structure Of Carboxypeptidase Y Inhibitor
Complexed With The Cognate Proteinase
pdb|1YSC|A Chain A, 2.8 Angstroms Structure Of Yeast Serine Carboxypeptidase
Length = 421
Score = 26.6 bits (57), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 9/69 (13%)
Query: 80 AAKDINNFYLEHGPKIFPQISRSNFSESIASSIDKRLLGPKYDGKYLRALVNELLGDVTV 139
A KD+ NF ++ F E + D + G Y G Y+ +E+L
Sbjct: 115 AGKDVYNFL---------ELFFDQFPEYVNKGQDFHIAGESYAGHYIPVFASEILSHKDR 165
Query: 140 KETLTNVVI 148
LT+V+I
Sbjct: 166 NFNLTSVLI 174
>pdb|2YK6|A Chain A, Structure Of Neisseria Los-Specific Sialyltransferase
(Nst), In Complex With Cdp
Length = 326
Score = 26.6 bits (57), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 53 DVVAGTSTGGLVTTMLTAPNKEGGPF--IAAKDINNFYLEHGPK 94
++ AG TGG V +L +P+KE AAK+ N Y+ P+
Sbjct: 191 ELKAGDETGGTVRILLGSPDKEMKEISEKAAKNFNIQYVAPHPR 234
>pdb|2YK7|A Chain A, Structure Of Neisseria Los-Specific Sialyltransferase
(Nst), In Complex With Cmp-3f-Neu5ac
Length = 326
Score = 26.6 bits (57), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 53 DVVAGTSTGGLVTTMLTAPNKEGGPF--IAAKDINNFYLEHGPK 94
++ AG TGG V +L +P+KE AAK+ N Y+ P+
Sbjct: 191 ELKAGDETGGTVRILLGSPDKEMKEISEKAAKNFNIQYVAPHPR 234
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
0.318 0.136 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,470,444
Number of Sequences: 62578
Number of extensions: 167549
Number of successful extensions: 419
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 411
Number of HSP's gapped (non-prelim): 13
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)