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= psy17954
(143 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U5C|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
pdb|3J16|C Chain C, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 236
Score = 162 bits (411), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 90/193 (46%), Positives = 108/193 (55%), Gaps = 61/193 (31%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
MKLNISYP G QK EI DEH++RVF+DKR+G EV +++GDE+KGY+ +ISGGNDKQG
Sbjct: 1 MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG 60
Query: 61 FPMKQG-----------------------------------------------------E 67
FPMKQG E
Sbjct: 61 FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE 120
Query: 68 IPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKLYKA 127
+ GLTDTT+P+RLGPKRA+ IRK F LSKEDDVR +VI+R E K + KA
Sbjct: 121 LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRR--------EVTKGEKTYTKA 172
Query: 128 PKIQRLITPVTLQ 140
PKIQRL+TP LQ
Sbjct: 173 PKIQRLVTPQRLQ 185
>pdb|2XZM|Y Chain Y, 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|Y Chain Y, 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 = 293
Score = 137 bits (344), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 84/192 (43%), Positives = 103/192 (53%), Gaps = 63/192 (32%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
MK NISYP TG QK +EI D+ K +F DK+MG EV D++GDE+KGY+ +I+GGNDK G
Sbjct: 1 MKFNISYPLTGAQKCIEIDDDKKCNIFMDKKMGQEVEGDTLGDEFKGYVFKIAGGNDKDG 60
Query: 61 FPMKQG-----------------------------------------------------E 67
FPMKQG E
Sbjct: 61 FPMKQGVMVRGRVRLLLSEGHSCFTSRRSGFRKRKSVRGCIVGPDMRVLALQIVKKGVAE 120
Query: 68 IPGLTDTTIPRRLGPKRASKIRKLFNLSKEDD---VRQYVIKRTLPPKPAKEGKKKVRKL 124
I GLT T+PR+LGPKRA+ I+KLF L KEDD +++ VI+RT K AK GK +
Sbjct: 121 IDGLTTVTLPRKLGPKRANNIKKLFGLKKEDDPILIKKSVIRRTF--KTAK-GKDRT--- 174
Query: 125 YKAPKIQRLITP 136
K PKIQRLITP
Sbjct: 175 -KCPKIQRLITP 185
>pdb|3ZEY|3 Chain 3, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 250
Score = 118 bits (295), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 78/192 (40%), Positives = 97/192 (50%), Gaps = 63/192 (32%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRV-FYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQ 59
MKLN++YP G K VE+ DE RV D R+G EV G+ ++GY ++ GG+DK+
Sbjct: 1 MKLNVAYPRNGTVKQVEVTDEVLRRVNLGDYRLGNEVDGAIFGEAFRGYTFKLRGGSDKE 60
Query: 60 GFPM--------------------------KQGE-------------------------- 67
GFPM QGE
Sbjct: 61 GFPMVQGVMAPSRVSLLVKRGAVGFNTFRGYQGERRRKSLRGCILGSDIAVLNVTVEKVG 120
Query: 68 ---IPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKL 124
I G+TD ++PRRLGPKRA+KIRKLFNL + DDVR+YVI+R K KEGKK
Sbjct: 121 EQPIEGVTDVSVPRRLGPKRANKIRKLFNLGRTDDVRKYVIRR----KVTKEGKK---DR 173
Query: 125 YKAPKIQRLITP 136
+KAPKIQRLIT
Sbjct: 174 FKAPKIQRLITS 185
>pdb|3J20|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 125
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 39/75 (52%), Gaps = 14/75 (18%)
Query: 1 MKLNISYPATGCQKLVEI--ADEHKLRVFYDKRMGMEVPADSI--------GDEWKGYI- 49
KL IS P +G K VEI A+ KL KR+G ++PA + G E+ +
Sbjct: 4 FKLVISDPKSGIAKQVEITGAETEKL---IGKRIGDQIPAKELNINLNELFGKEFPEDVK 60
Query: 50 VRISGGNDKQGFPMK 64
+ I GG DK GFPM+
Sbjct: 61 LEIRGGTDKDGFPMR 75
>pdb|3TD3|A Chain A, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD3|B Chain B, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD3|C Chain C, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD3|D Chain D, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD3|E Chain E, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD3|F Chain F, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD3|G Chain G, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD3|H Chain H, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Glycine
pdb|3TD4|A Chain A, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD4|B Chain B, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD4|C Chain C, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD4|D Chain D, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD4|E Chain E, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD4|F Chain F, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD4|G Chain G, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD4|H Chain H, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With Diaminopimelate
pdb|3TD5|A Chain A, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
pdb|3TD5|B Chain B, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
pdb|3TD5|C Chain C, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
pdb|3TD5|D Chain D, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
pdb|3TD5|E Chain E, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
pdb|3TD5|F Chain F, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
pdb|3TD5|G Chain G, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
pdb|3TD5|H Chain H, Crystal Structure Of Ompa-Like Domain From Acinetobacter
Baumannii In Complex With
L-Ala-Gamma-D-Glu-M-Dap-D-Ala-D-Ala
Length = 123
Score = 29.3 bits (64), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 49/112 (43%), Gaps = 17/112 (15%)
Query: 23 KLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQGEIPGLTDTTIPRRLGP 82
+LRVF+D +I D++K I +++ +P I G TD T PR+L
Sbjct: 13 ELRVFFD------TNKSNIKDQYKPEIAKVA--EKLSEYPNATARIEGHTDNTGPRKLNE 64
Query: 83 K----RASKIRK-LFNLSKEDDVR----QYVIKRTLPPKPAKEGKKKVRKLY 125
+ RA+ ++ L N D R + + + KEG+ R+++
Sbjct: 65 RLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVF 116
>pdb|2PO3|A Chain A, Crystal Structure Analysis Of Desi In The Presence Of Its
Tdp-Sugar Product
pdb|2PO3|B Chain B, Crystal Structure Analysis Of Desi In The Presence Of Its
Tdp-Sugar Product
Length = 424
Score = 29.3 bits (64), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 10 TGCQKLVEIADEHKLRVFYD--KRMGMEV---PADSIGD 43
+L ++ADEH LR+++D +G V PA S+GD
Sbjct: 152 CAADQLRKVADEHGLRLYFDAAHALGCAVDGRPAGSLGD 190
>pdb|3ASW|A Chain A, Structural And Biochemical Characterization Of Clfb:ligand
Interactions
Length = 328
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 2 KLNISYPAT-GCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
KL+ SY A L E+ D+ K R++Y+ V + GD K Y+V + G D G
Sbjct: 238 KLSESYYADPNDSNLKEVTDQFKNRIYYEHP---NVASIKFGDITKTYVVLVEGHYDNTG 294
Query: 61 FPMK 64
+K
Sbjct: 295 KNLK 298
>pdb|3AU0|A Chain A, Structural And Biochemical Characterization Of Clfb:ligand
Interactions
Length = 339
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 2 KLNISYPAT-GCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
KL+ SY A L E+ D+ K R++Y+ V + GD K Y+V + G D G
Sbjct: 239 KLSESYYADPNDSNLKEVTDQFKNRIYYEHP---NVASIKFGDITKTYVVLVEGHYDNTG 295
Query: 61 FPMK 64
+K
Sbjct: 296 KNLK 299
>pdb|3AT0|A Chain A, Structural And Biochemical Characterization Of Clfb:ligand
Interactions
Length = 338
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 2 KLNISYPAT-GCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
KL+ SY A L E+ D+ K R++Y+ V + GD K Y+V + G D G
Sbjct: 238 KLSESYYADPNDSNLKEVTDQFKNRIYYEHP---NVASIKFGDITKTYVVLVEGHYDNTG 294
Query: 61 FPMK 64
+K
Sbjct: 295 KNLK 298
>pdb|3DF8|A Chain A, The Crystal Structure Of A Possible Hxlr Family
Transcriptional Factor From Thermoplasma Volcanium Gss1
Length = 111
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 41 IGDEWKGYIVRISG-GNDKQGFPMKQGEIPGLTDTTIPRRL 80
+G ++ I+ + G G+ +Q F + IPG++ T + RR+
Sbjct: 24 LGKKYTXLIISVLGNGSTRQNFNDIRSSIPGISSTILSRRI 64
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 0.138 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,275,764
Number of Sequences: 62578
Number of extensions: 169333
Number of successful extensions: 458
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 445
Number of HSP's gapped (non-prelim): 17
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
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: 46 (22.3 bits)