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= 025671
(249 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PL9|A Chain A, Crystal Structure Of Spinach Minor Light-Harvesting
Complex Cp29 At 2.80 Angstrom Resolution
Length = 243
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 18/92 (19%)
Query: 154 IKRFHLPEAELLNGRAAMIGFFMAYLVDSLTGV-----GLVDQM--SNFFCKTLLF---- 202
++RF E EL++GR AM+ A V+ LTG+ G V+ + S++ + L F
Sbjct: 89 LQRFR--ECELIHGRWAMLATLGALTVEGLTGITWQDAGKVELIEGSSYLGQPLPFSMTT 146
Query: 203 -----VAVVGVLLIRKNEDIETLKKLLEETTF 229
V V+G + ++N +++T K+L TF
Sbjct: 147 LIWIEVLVIGYIEFQRNAELDTEKRLYPGGTF 178
>pdb|1P8T|A Chain A, Crystal Structure Of Nogo-66 Receptor
Length = 285
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 137 NDDPVIFDTSIVPWWAWIKRF 157
ND+P + D P WAW+++F
Sbjct: 232 NDNPWVCDCRARPLWAWLQKF 252
>pdb|1OZN|A Chain A, 1.5a Crystal Structure Of The Nogo Receptor Ligand Binding
Domain Reveals A Convergent Recognition Scaffold
Mediating Inhibition Of Myelination
Length = 285
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 137 NDDPVIFDTSIVPWWAWIKRF 157
ND+P + D P WAW+++F
Sbjct: 233 NDNPWVCDCRARPLWAWLQKF 253
>pdb|3KJ4|A Chain A, Structure Of Rat Nogo Receptor Bound To 1d9 Antagonist
Antibody
pdb|3KJ4|D Chain D, Structure Of Rat Nogo Receptor Bound To 1d9 Antagonist
Antibody
Length = 286
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 137 NDDPVIFDTSIVPWWAWIKRF 157
ND+P + D P WAW+++F
Sbjct: 232 NDNPWVCDCRARPLWAWLQKF 252
>pdb|3B8X|A Chain A, Crystal Structure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188n
Mutant With Bound Gdp-Perosamine
pdb|3B8X|B Chain B, Crystal Structure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188n
Mutant With Bound Gdp-Perosamine
Length = 390
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 25/130 (19%), Positives = 56/130 (43%), Gaps = 19/130 (14%)
Query: 73 PTESNGAVEAPEVKAVNKFEDPKWVNGTWDLKQF---------QKNGQTDW---DAVI-- 118
P E +GA+ ++K + +F + N + L +F Q+ G++ W +I
Sbjct: 253 PLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKK 312
Query: 119 DAEARRRKWLENSPESSSNDDPVIF-----DTSIVPWWAWIKRFHLPEAELLNGRAAMIG 173
D+ R++ +EN + P++ +T ++ ++ + ++ AE L+ +G
Sbjct: 313 DSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVG 372
Query: 174 FFMAYLVDSL 183
L D +
Sbjct: 373 NHQIELFDEI 382
>pdb|2R0T|A Chain A, Crystal Sructure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase With A Trapped
Plp-Glutamate Geminal Diamine
pdb|2R0T|B Chain B, Crystal Sructure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase With A Trapped
Plp-Glutamate Geminal Diamine
Length = 390
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 25/130 (19%), Positives = 56/130 (43%), Gaps = 19/130 (14%)
Query: 73 PTESNGAVEAPEVKAVNKFEDPKWVNGTWDLKQF---------QKNGQTDW---DAVI-- 118
P E +GA+ ++K + +F + N + L +F Q+ G++ W +I
Sbjct: 253 PLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKK 312
Query: 119 DAEARRRKWLENSPESSSNDDPVIF-----DTSIVPWWAWIKRFHLPEAELLNGRAAMIG 173
D+ R++ +EN + P++ +T ++ ++ + ++ AE L+ +G
Sbjct: 313 DSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVG 372
Query: 174 FFMAYLVDSL 183
L D +
Sbjct: 373 NHQIELFDEI 382
>pdb|2GMS|A Chain A, E Coli Gdp-4-Keto-6-Deoxy-D-Mannose-3-Dehydratase With
Bound Hydrated Plp
pdb|2GMS|B Chain B, E Coli Gdp-4-Keto-6-Deoxy-D-Mannose-3-Dehydratase With
Bound Hydrated Plp
pdb|2GMU|A Chain A, Crystal Structure Of E Coli
Gdp-4-Keto-6-Deoxy-D-Mannose-3- Dehydratase Complexed
With Plp-Glutamate Ketimine Intermediate
pdb|2GMU|B Chain B, Crystal Structure Of E Coli
Gdp-4-Keto-6-Deoxy-D-Mannose-3- Dehydratase Complexed
With Plp-Glutamate Ketimine Intermediate
Length = 390
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 25/130 (19%), Positives = 56/130 (43%), Gaps = 19/130 (14%)
Query: 73 PTESNGAVEAPEVKAVNKFEDPKWVNGTWDLKQF---------QKNGQTDW---DAVI-- 118
P E +GA+ ++K + +F + N + L +F Q+ G++ W +I
Sbjct: 253 PLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKK 312
Query: 119 DAEARRRKWLENSPESSSNDDPVIF-----DTSIVPWWAWIKRFHLPEAELLNGRAAMIG 173
D+ R++ +EN + P++ +T ++ ++ + ++ AE L+ +G
Sbjct: 313 DSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVG 372
Query: 174 FFMAYLVDSL 183
L D +
Sbjct: 373 NHQIELFDEI 382
>pdb|3GR9|A Chain A, Crystal Structure Of Cold H188k S187n
pdb|3GR9|B Chain B, Crystal Structure Of Cold H188k S187n
pdb|3GR9|C Chain C, Crystal Structure Of Cold H188k S187n
pdb|3GR9|D Chain D, Crystal Structure Of Cold H188k S187n
pdb|3GR9|E Chain E, Crystal Structure Of Cold H188k S187n
pdb|3GR9|F Chain F, Crystal Structure Of Cold H188k S187n
pdb|3GR9|G Chain G, Crystal Structure Of Cold H188k S187n
pdb|3GR9|H Chain H, Crystal Structure Of Cold H188k S187n
Length = 390
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 25/130 (19%), Positives = 56/130 (43%), Gaps = 19/130 (14%)
Query: 73 PTESNGAVEAPEVKAVNKFEDPKWVNGTWDLKQF---------QKNGQTDW---DAVI-- 118
P E +GA+ ++K + +F + N + L +F Q+ G++ W +I
Sbjct: 253 PLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKK 312
Query: 119 DAEARRRKWLENSPESSSNDDPVIF-----DTSIVPWWAWIKRFHLPEAELLNGRAAMIG 173
D+ R++ +EN + P++ +T ++ ++ + ++ AE L+ +G
Sbjct: 313 DSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVG 372
Query: 174 FFMAYLVDSL 183
L D +
Sbjct: 373 NHQIELFDEI 382
>pdb|3LW5|4 Chain 4, Improved Model Of Plant Photosystem I
Length = 166
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 161 EAELLNGRAAMIGFFMAYLVDSLTGVGLVD 190
+AEL+NGR AM+G L + T +G+++
Sbjct: 13 QAELVNGRWAMLGVAGMLLPEVFTSIGIIN 42
>pdb|2O01|4 Chain 4, The Structure Of A Plant Photosystem I Supercomplex At 3.4
Angstrom Resolution
Length = 165
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 161 EAELLNGRAAMIGFFMAYLVDSLTGVGLVD 190
+AEL+NGR AM+G L + T +G+++
Sbjct: 9 QAELVNGRWAMLGVAGMLLPEVFTSIGIIN 38
>pdb|2WSC|4 Chain 4, Improved Model Of Plant Photosystem I
pdb|2WSE|4 Chain 4, Improved Model Of Plant Photosystem I
pdb|2WSF|4 Chain 4, Improved Model Of Plant Photosystem I
Length = 251
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 161 EAELLNGRAAMIGFFMAYLVDSLTGVGLVD 190
+AEL+NGR AM+G L + T +G+++
Sbjct: 93 QAELVNGRWAMLGVAGMLLPEVFTSIGIIN 122
>pdb|1SQF|A Chain A, The Crystal Structure Of E. Coli Fmu Binary Complex With
S- Adenosylmethionine At 2.1 A Resolution
pdb|1SQG|A Chain A, The Crystal Structure Of The E. Coli Fmu Apoenzyme At 1.65
A Resolution
Length = 429
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 93 DPKWVNGTWDLKQFQKNGQTDWDAVIDAEARRRK-WLENSPESSSND 138
D ++++ +W LK+ QK W ++++A +R WL + S D
Sbjct: 140 DARYLHPSWLLKRLQKAYPEQWQSIVEANNQRPPMWLRINRTHHSRD 186
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
0.315 0.130 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,247,227
Number of Sequences: 62578
Number of extensions: 293704
Number of successful extensions: 699
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 688
Number of HSP's gapped (non-prelim): 17
length of query: 249
length of database: 14,973,337
effective HSP length: 96
effective length of query: 153
effective length of database: 8,965,849
effective search space: 1371774897
effective search space used: 1371774897
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)