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= 024952
(260 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3J20|J Chain J, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 127
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 15/66 (22%)
Query: 194 LEIIGVKKNPNGPMYTSLGVITKGTIIEVNVSELGLVTPAGKVVWGKYAQVTNNPENDGC 253
+ II V +NP + +ITKG IIE + + A+VT+ P DG
Sbjct: 75 VRIIRVIENPANRQFARRNIITKGAIIETEIGK---------------AKVTSRPGQDGV 119
Query: 254 INAVLL 259
+NA+LL
Sbjct: 120 VNAILL 125
>pdb|2KCY|A Chain A, Solution Structure Of Ribosomal Protein S8e From
Methanothermobacter Thermautotrophicus,
Northeaststructural Genomics Consortium (Nesg) Target
Tr71d
pdb|2KCP|A Chain A, Solution Structure Of 30s Ribosomal Protein S8e; From
Methanothermobacter Thermautotrophicus,
Northeaststructural Genomics Consortium (Nesg) Target
Tr71d
Length = 98
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 15/81 (18%)
Query: 179 TKAHVTHPELKCTFNLEIIGVKKNPNGPMYTSLGVITKGTIIEVNVSELGLVTPAGKVVW 238
T+ +V PE EI V +N P + +IT+G ++E N+ +
Sbjct: 23 TRINVVDPETGKVEIAEIRNVVENTANPHFVRRNIITRGAVVETNLGNV----------- 71
Query: 239 GKYAQVTNNPENDGCINAVLL 259
+VT+ P DG IN VL+
Sbjct: 72 ----RVTSRPGQDGVINGVLI 88
>pdb|2KCO|A Chain A, Solution Nmr Structure Of Ribosomal Protein Sso0164 From
Sulfolobus Solfataricus. Northeast Structural Genomics
Consortium (Nesg) Target Sst4
Length = 133
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 35/81 (43%), Gaps = 15/81 (18%)
Query: 179 TKAHVTHPELKCTFNLEIIGVKKNPNGPMYTSLGVITKGTIIEVNVSELGLVTPAGKVVW 238
T A+V P ++I+ + + P G+I +G I +E GL
Sbjct: 61 TTANVLDPATNTAKKVKILEILETPANKELARRGIIIRGAKIR---TEAGL--------- 108
Query: 239 GKYAQVTNNPENDGCINAVLL 259
A VT+ P DG INAVLL
Sbjct: 109 ---AVVTSRPGQDGVINAVLL 126
>pdb|3ACF|A Chain A, Crystal Structure Of Carbohydrate-Binding Module Family 28
From Clostridium Josui Cel5a In A Ligand-Free Form
pdb|3ACG|A Chain A, Crystal Structure Of Carbohydrate-Binding Module Family 28
From Clostridium Josui Cel5a In Complex With Cellobiose
pdb|3ACH|A Chain A, Crystal Structure Of Carbohydrate-Binding Module Family 28
From Clostridium Josui Cel5a In Complex With
Cellotetraose
pdb|3ACI|A Chain A, Crystal Structure Of Carbohydrate-Binding Module Family 28
From Clostridium Josui Cel5a In Complex With
Cellopentaose
Length = 203
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 105 TIKQKRKEKAGKWEVPLPKVRPV 127
TIK + KA WEV P+V+PV
Sbjct: 53 TIKDANESKAISWEVKYPEVKPV 75
>pdb|3E6M|A Chain A, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss.
pdb|3E6M|B Chain B, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss.
pdb|3E6M|C Chain C, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss.
pdb|3E6M|D Chain D, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss.
pdb|3E6M|E Chain E, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss.
pdb|3E6M|F Chain F, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss.
pdb|3E6M|G Chain G, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss.
pdb|3E6M|H Chain H, The Crystal Structure Of A Marr Family Transcriptional
Regulator From Silicibacter Pomeroyi Dss
Length = 161
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 64 TLAMHEESSSRRKVDDEVQEGAVPAYLLDRENTTRAKVLSNTIKQKRKE 112
TL + E+S++ R VD V EG + D + R VL+ K+K E
Sbjct: 75 TLGVXEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAE 123
>pdb|3O1A|A Chain A, Structure Of Oxye (Cyp165d3), A Cytochrome P450 Involved
In Teicoplanin Biosynthesis
Length = 417
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 61 MKKTLAMHEESSSRRKVDDEVQEGAVPAYL 90
++ LA HE SS R VDDE +P L
Sbjct: 83 VRAILADHERFSSMRPVDDEADRALLPGIL 112
>pdb|3OO3|A Chain A, Crystal Structure Of The Orf6 (Cyp165d3) Monooxygenase
Involved In Teicoplanin Biosynthesis
Length = 384
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 61 MKKTLAMHEESSSRRKVDDEVQEGAVPAYL 90
++ LA HE SS R VDDE +P L
Sbjct: 50 VRAILADHERFSSMRPVDDEADRALLPGIL 79
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
0.317 0.133 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,809,960
Number of Sequences: 62578
Number of extensions: 320014
Number of successful extensions: 883
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 873
Number of HSP's gapped (non-prelim): 11
length of query: 260
length of database: 14,973,337
effective HSP length: 97
effective length of query: 163
effective length of database: 8,903,271
effective search space: 1451233173
effective search space used: 1451233173
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)