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= 028873
(202 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PY6|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein From
Brucella Melitensis Bound To Gmp
pdb|3PY5|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein From
Brucella Melitensis Bound To Amp
pdb|3QH8|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein Bound
To Amp From Brucella Melitensis, Long Wavelength
Synchrotron Data
Length = 274
Score = 79.0 bits (193), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 58/191 (30%), Positives = 94/191 (49%), Gaps = 18/191 (9%)
Query: 18 GLDDLRDWTNNVQRHIPIYVAMRDFEVMKKTHYYLVDTSGIIPGAAVSEL--QFNIIDEE 75
G+DDLR + + R + +Y + T Y +T G++ + +I E
Sbjct: 96 GIDDLRTYVVDNGRLMDVYANRLTRNRLYDTFGYCFETP---VGSSYPPILSMHDIAPET 152
Query: 76 PFTVQD----LKITPLPVWHGAGYRSLGFRFGNICYISDVSEIPEETYPFLQDCEILIMD 131
PF+++ ++ P HG SLGFR G++ Y +DVS PE++ +++D ++LI+
Sbjct: 153 PFSIEGAGGAIRFEPFSQVHGD-IESLGFRIGSVVYCTDVSAFPEQSLQYIKDADVLIIG 211
Query: 132 ALRPDRSSSTHFGLPRALEEVRKIQPKRTLFIGMMHLMDHEKVNEELLKLMETEGLDVQL 191
AL+ R +HF L ALE + K+ PKR + M +D+E V E +E
Sbjct: 212 ALQ-YRPHPSHFSLGEALEWIEKLSPKRAILTHMHVPLDYETVMRETPHHVEP------- 263
Query: 192 SYDGLRVPVML 202
YDGLR V +
Sbjct: 264 GYDGLRFEVAV 274
>pdb|3MD7|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein Bound
To Gmp From Brucella Melitensis
Length = 293
Score = 78.6 bits (192), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 58/191 (30%), Positives = 94/191 (49%), Gaps = 18/191 (9%)
Query: 18 GLDDLRDWTNNVQRHIPIYVAMRDFEVMKKTHYYLVDTSGIIPGAAVSEL--QFNIIDEE 75
G+DDLR + + R + +Y + T Y +T G++ + +I E
Sbjct: 115 GIDDLRTYVVDNGRLMDVYANRLTRNRLYDTFGYCFETP---VGSSYPPILSMHDIAPET 171
Query: 76 PFTVQD----LKITPLPVWHGAGYRSLGFRFGNICYISDVSEIPEETYPFLQDCEILIMD 131
PF+++ ++ P HG SLGFR G++ Y +DVS PE++ +++D ++LI+
Sbjct: 172 PFSIEGAGGAIRFEPFSQVHGD-IESLGFRIGSVVYCTDVSAFPEQSLQYIKDADVLIIG 230
Query: 132 ALRPDRSSSTHFGLPRALEEVRKIQPKRTLFIGMMHLMDHEKVNEELLKLMETEGLDVQL 191
AL+ R +HF L ALE + K+ PKR + M +D+E V E +E
Sbjct: 231 ALQ-YRPHPSHFSLGEALEWIEKLSPKRAILTHMHVPLDYETVMRETPHHVEP------- 282
Query: 192 SYDGLRVPVML 202
YDGLR V +
Sbjct: 283 GYDGLRFEVAV 293
>pdb|3G1P|A Chain A, Crystals Structure Of Phnp From E.Coli K-12
pdb|3G1P|B Chain B, Crystals Structure Of Phnp From E.Coli K-12
pdb|3P2U|A Chain A, Crystal Structure Of Phnp In Complex With Orthovanadate
pdb|3P2U|B Chain B, Crystal Structure Of Phnp In Complex With Orthovanadate
Length = 258
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 18/136 (13%)
Query: 75 EPFTV---QDLKITPLPVWHGA---GYRSLGFRFGNICYISDVSEIPEETYPFLQDC--E 126
EPF V Q L++TPLP+ H GY L + ++SD + +PE+T FL++ +
Sbjct: 124 EPFVVFDLQGLQVTPLPLNHSKLTFGYL-LETAHSRVAWLSDTAGLPEKTLKFLRNNQPQ 182
Query: 127 ILIMDALRPDRSSS--THFGLPRALEEVRKIQPKRTLFIGMMHLMDHEKVNEELLKLMET 184
+++MD P R+ + H L L + I+ R + + H D + L E
Sbjct: 183 VMVMDCSHPPRADAPRNHCDLNTVLALNQVIRSPRVILTHISHQFDAWLMENALPSGFE- 241
Query: 185 EGLDVQLSYDGLRVPV 200
+ +DG+ + V
Sbjct: 242 ------VGFDGMEIGV 251
>pdb|3NCO|A Chain A, Crystal Structure Of Fncel5a From F. Nodosum Rt17-B1
pdb|3NCO|B Chain B, Crystal Structure Of Fncel5a From F. Nodosum Rt17-B1
Length = 320
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 146 PRALEEVRKIQPKRTLFIGMMHLMDHEKVNEELLKLMETEGLDVQLSY 193
P+ L E+RK P R + I + + ++ V E LKL++ + + V Y
Sbjct: 159 PKVLGEIRKTNPSRIVIIDVPNWSNYSYVRE--LKLVDDKNIIVSFHY 204
>pdb|3RJX|A Chain A, Crystal Structure Of Hyperthermophilic
Endo-Beta-1,4-Glucanase
Length = 320
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 146 PRALEEVRKIQPKRTLFIGMMHLMDHEKVNEELLKLMETEGLDVQLSY 193
P+ L E+RK P R + I + + ++ V E LKL++ + + V Y
Sbjct: 159 PKVLGEIRKTNPSRIVIIDVPNWSNYSYVRE--LKLVDDKNIIVSFHY 204
>pdb|3RJY|A Chain A, Crystal Structure Of Hyperthermophilic
Endo-Beta-1,4-Glucanase In Complex With Substrate
Length = 320
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 146 PRALEEVRKIQPKRTLFIGMMHLMDHEKVNEELLKLMETEGLDVQLSY 193
P+ L E+RK P R + I + + ++ V E LKL++ + + V Y
Sbjct: 159 PKVLGEIRKTNPSRIVIIDVPNWSNYSYVRE--LKLVDDKNIIVSFHY 204
>pdb|1TKW|B Chain B, The Transient Complex Of Poplar Plastocyanin With Turnip
Cytochrome F Determined With Paramagnetic Nmr
pdb|1HCZ|A Chain A, Lumen-Side Domain Of Reduced Cytochrome F At-35 Degrees
Celsius
Length = 252
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 57 GIIPGAAVSELQFNIIDEEPFTVQDLKITPLPVWHGAGYRSLG 99
G +PG SE+ F I+ +P T +D+ P++ G G R G
Sbjct: 116 GPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVG-GNRGRG 157
>pdb|1CTM|A Chain A, Crystal Structure Of Chloroplast Cytochrome F Reveals A
Novel Cytochrome Fold And Unexpected Heme Ligation
pdb|2PCF|B Chain B, The Complex Of Cytochrome F And Plastocyanin Determined
With Paramagnetic Nmr. Based On The Structures Of
Cytochrome F And Plastocyanin, 10 Structures
Length = 250
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 57 GIIPGAAVSELQFNIIDEEPFTVQDLKITPLPVWHGAGYRSLG 99
G +PG SE+ F I+ +P T +D+ P++ G G R G
Sbjct: 116 GPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVG-GNRGRG 157
>pdb|3GMI|A Chain A, Crystal Structure Of A Protein Of Unknown Function From
Methanocaldococcus Jannaschii
Length = 357
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 149 LEEVRKIQPKRTLFIGMMHLMDHEKVNEELLKLMETEGLDVQLSYD 194
E+++ + PK TL I + L D+ K+NE +LK E L+ YD
Sbjct: 241 FEDIKNMLPKTTLSI-LKELYDNGKLNELILKRFEDRILETANEYD 285
>pdb|2D40|A Chain A, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
pdb|2D40|B Chain B, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
pdb|2D40|C Chain C, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
pdb|2D40|D Chain D, Crystal Structure Of Z3393 From Escherichia Coli O157:h7
Length = 354
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 11/65 (16%)
Query: 33 IPIYVAMRDFEVMKKTHYYLVDTSGIIPGAAVSELQFNIIDEEPFTVQDLKITPLPVWHG 92
+P A R T Y++V+ SG + II E F+ I +P WHG
Sbjct: 275 LPKGFASRVARTTDSTIYHVVEGSGQV-----------IIGNETFSFSAKDIFVVPTWHG 323
Query: 93 AGYRS 97
+++
Sbjct: 324 VSFQT 328
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
0.324 0.142 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,029,270
Number of Sequences: 62578
Number of extensions: 245657
Number of successful extensions: 569
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 560
Number of HSP's gapped (non-prelim): 14
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)