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= psy1800
(81 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 265
Score = 87.4 bits (215), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 40/63 (63%), Positives = 48/63 (76%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
GN+ M+TGGRN GRVG + NRE+H GSF+ +HV+D GH FATRL NVF IGKG K + S
Sbjct: 178 GNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVS 237
Query: 64 KPK 66
PK
Sbjct: 238 LPK 240
>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5C|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 261
Score = 83.6 bits (205), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 48/63 (76%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
G L +TGGRNLGR+GT+V++ERH G FD+VH+KD + F TRLNNVF+IG+ K + S
Sbjct: 178 GKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYIS 237
Query: 64 KPK 66
PK
Sbjct: 238 LPK 240
>pdb|2XZM|W Chain W, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|W Chain W, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 260
Score = 78.2 bits (191), Expect = 1e-15, Method: Composition-based stats.
Identities = 33/62 (53%), Positives = 45/62 (72%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
GN+C I G N+GRVG + + E+H GSFDI HVKD G+ FATRL N+F++G+G K++
Sbjct: 180 GNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIE 239
Query: 64 KP 65
P
Sbjct: 240 LP 241
>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 273
Score = 74.3 bits (181), Expect = 1e-14, Method: Composition-based stats.
Identities = 31/53 (58%), Positives = 41/53 (77%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGK 56
G + M+TGG N GR+G +V+ ERHPG+FDI +KD +GH FATR N+F+IGK
Sbjct: 175 GKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRATNIFVIGK 227
>pdb|3J20|E Chain E, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 243
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 4 GNLCMITGGRNLGRVGTVVNRERHP-GSFDIVHVKDGNGHVFATRLNNVFIIG 55
G +T G+N+ R G +V +R P G D+V ++D G +F T F++G
Sbjct: 182 GAYVFVTQGKNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVG 234
>pdb|3KBG|A Chain A, Crystal Structure Of The 30s Ribosomal Protein S4e From
Thermoplasma Acidophilum. Northeast Structural Genomics
Consortium Target Tar28
Length = 213
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 12/76 (15%)
Query: 3 PGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAF 61
PGN IT G ++ + GT+ E G S ++VH ++G F+T ++VF IG +F
Sbjct: 141 PGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQEG----FSTIKDHVFXIGSSKFSF 196
Query: 62 CSKPKRNFVSPRQTCP 77
+SP + P
Sbjct: 197 V-------LSPEEVIP 205
>pdb|2V0R|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Ltx) Of
The Targeting Line-1 Retrotransposon Endonuclease
pdb|2V0R|B Chain B, Crystal Structure Of A Hairpin Exchange Variant (Ltx) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 240
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 22 VNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70
+ R HP S + +V+ +GHV ++++++ G+KA SK KR +
Sbjct: 180 IYRTLHPKSTEYTYVRVRDGHVSQSKIDHIV----GSKALLSKCKRTEI 224
>pdb|3EDD|A Chain A, Structural Base For Cyclodextrin Hydrolysis
pdb|3EDD|B Chain B, Structural Base For Cyclodextrin Hydrolysis
Length = 601
Score = 26.6 bits (57), Expect = 3.4, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 25 ERHPGSFDIVHVKDGNGHVFATRL 48
E PGSFDIV DG + RL
Sbjct: 67 EAQPGSFDIVFKGDGRSERYRYRL 90
>pdb|3EDE|A Chain A, Structural Base For Cyclodextrin Hydrolysis
pdb|3EDE|B Chain B, Structural Base For Cyclodextrin Hydrolysis
Length = 601
Score = 26.6 bits (57), Expect = 3.4, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 25 ERHPGSFDIVHVKDGNGHVFATRL 48
E PGSFDIV DG + RL
Sbjct: 67 EAQPGSFDIVFKGDGRSERYRYRL 90
>pdb|3EDF|A Chain A, Structural Base For Cyclodextrin Hydrolysis
pdb|3EDF|B Chain B, Structural Base For Cyclodextrin Hydrolysis
pdb|3EDJ|A Chain A, Structural Base For Cyclodextrin Hydrolysis
pdb|3EDJ|B Chain B, Structural Base For Cyclodextrin Hydrolysis
pdb|3EDK|A Chain A, Structural Base For Cyclodextrin Hydrolysis
pdb|3EDK|B Chain B, Structural Base For Cyclodextrin Hydrolysis
Length = 601
Score = 26.6 bits (57), Expect = 3.5, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 25 ERHPGSFDIVHVKDGNGHVFATRL 48
E PGSFDIV DG + RL
Sbjct: 67 EAQPGSFDIVFKGDGRSERYRYRL 90
>pdb|4D9S|A Chain A, Crystal Structure Of Arabidopsis Thaliana Uvr8 (Uv
Resistance Locus 8)
pdb|4D9S|B Chain B, Crystal Structure Of Arabidopsis Thaliana Uvr8 (Uv
Resistance Locus 8)
Length = 406
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 12 GRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFA-TRLNNVFIIGKGT 58
G NL + V + R P +V V G H A T NNVF G+GT
Sbjct: 312 GNNLDQCSPV--QVRFPDDQKVVQVSCGWRHTLAVTERNNVFAWGRGT 357
>pdb|1H3G|A Chain A, Cyclomaltodextrinase From Flavobacterium Sp. No. 92:
From Dna Sequence To Protein Structure
pdb|1H3G|B Chain B, Cyclomaltodextrinase From Flavobacterium Sp. No. 92:
From Dna Sequence To Protein Structure
Length = 601
Score = 26.6 bits (57), Expect = 3.8, Method: Composition-based stats.
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 25 ERHPGSFDIVHVKDGNGHVFATRL 48
E PGSFDIV DG + RL
Sbjct: 67 EAQPGSFDIVFKGDGRSERYRYRL 90
>pdb|4DNW|A Chain A, Crystal Structure Of Uvb-Resistance Protein Uvr8
pdb|4DNW|B Chain B, Crystal Structure Of Uvb-Resistance Protein Uvr8
Length = 374
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 12 GRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFA-TRLNNVFIIGKGT 58
G NL + V + R P +V V G H A T NNVF G+GT
Sbjct: 300 GNNLDQCSPV--QVRFPDDQKVVQVSCGWRHTLAVTERNNVFAWGRGT 345
>pdb|4DNV|A Chain A, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
pdb|4DNV|B Chain B, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
pdb|4DNV|C Chain C, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
pdb|4DNV|D Chain D, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
Length = 370
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 12 GRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFA-TRLNNVFIIGKGT 58
G NL + V + R P +V V G H A T NNVF G+GT
Sbjct: 300 GNNLDQCSPV--QVRFPDDQKVVQVSCGWRHTLAVTERNNVFAWGRGT 345
>pdb|4DNU|A Chain A, Crystal Structure Of The W285a Mutant Of Uvb-Resistance
Protein Uvr8
Length = 372
Score = 26.2 bits (56), Expect = 4.5, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 12 GRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFA-TRLNNVFIIGKGT 58
G NL + V + R P +V V G H A T NNVF G+GT
Sbjct: 302 GNNLDQCSPV--QVRFPDDQKVVQVSCGWRHTLAVTERNNVFAWGRGT 347
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
0.325 0.142 0.454
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,699,908
Number of Sequences: 62578
Number of extensions: 98554
Number of successful extensions: 286
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 276
Number of HSP's gapped (non-prelim): 15
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)