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= psy3462
(795 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|XX Chain x, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 125
Score = 101 bits (252), Expect = 1e-21, Method: Composition-based stats.
Identities = 45/66 (68%), Positives = 56/66 (84%)
Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
+ +NEVVTR+YTI++HKR+H VGFKKRAPRA+K +R F K+MGT DVRIDTRLNK +W
Sbjct: 14 RSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVW 73
Query: 177 SKGINN 182
+KGI N
Sbjct: 74 AKGIRN 79
>pdb|2GO5|6 Chain 6, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
pdb|2J37|6 Chain 6, Model Of Mammalian Srp Bound To 80s Rncs
Length = 123
Score = 90.9 bits (224), Expect = 3e-18, Method: Composition-based stats.
Identities = 42/70 (60%), Positives = 53/70 (75%), Gaps = 3/70 (4%)
Query: 111 KKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTR 170
+ P +K +EVVTR+YT+++HKRLH FKK+AP AIK +R F +K MGT DVRID +
Sbjct: 6 RAPGPRK---DEVVTREYTVNLHKRLHGCTFKKKAPNAIKEIRKFAQKAMGTNDVRIDVK 62
Query: 171 LNKHIWSKGI 180
LNKHIWS GI
Sbjct: 63 LNKHIWSSGI 72
>pdb|3IZR|GG Chain g, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 123
Score = 84.7 bits (208), Expect = 2e-16, Method: Composition-based stats.
Identities = 40/69 (57%), Positives = 52/69 (75%), Gaps = 2/69 (2%)
Query: 111 KKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTR 170
K+ A +K +EVVTR+YTI++HKRLH FKK+AP AIK +R F +K MGT D+RID +
Sbjct: 5 KRGAGTRK--DEVVTREYTINLHKRLHGCTFKKKAPNAIKEIRKFAQKAMGTTDIRIDVK 62
Query: 171 LNKHIWSKG 179
LNK IW+ G
Sbjct: 63 LNKAIWTNG 71
>pdb|1S1I|W Chain W, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 112
Score = 83.6 bits (205), Expect = 4e-16, Method: Composition-based stats.
Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKG 179
L +VVTR+YTI++HKRLH V FKKRAPRA+K ++ F K MGT+DVR+ LN+ IW +G
Sbjct: 3 LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRG 62
Query: 180 I 180
+
Sbjct: 63 V 63
>pdb|2WW9|M Chain M, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|M Chain M, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|M Chain M, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
pdb|3IZS|GG Chain g, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|AA Chain a, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|AA Chain a, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|DD Chain d, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 113
Score = 83.6 bits (205), Expect = 4e-16, Method: Composition-based stats.
Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKG 179
L +VVTR+YTI++HKRLH V FKKRAPRA+K ++ F K MGT+DVR+ LN+ IW +G
Sbjct: 4 LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRG 63
Query: 180 I 180
+
Sbjct: 64 V 64
>pdb|4A17|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 111
Score = 79.3 bits (194), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 35/56 (62%), Positives = 44/56 (78%)
Query: 127 DYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINN 182
D T+++HK+ HK+ FKK+APRAI+ + A KK MGT+DVRIDT LNK IWS GI N
Sbjct: 10 DTTVNLHKQCHKISFKKKAPRAIREIVAIAKKTMGTDDVRIDTELNKFIWSNGIRN 65
>pdb|3JYW|W Chain W, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 79
Score = 75.9 bits (185), Expect = 8e-14, Method: Composition-based stats.
Identities = 33/56 (58%), Positives = 44/56 (78%)
Query: 125 TRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
TR+YTI++HKRLH V FKKRAPRA+K ++ F K MGT+DVR+ LN+ IW +G+
Sbjct: 1 TREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGV 56
>pdb|3ZF7|HH Chain h, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 188
Score = 60.5 bits (145), Expect = 4e-09, Method: Composition-based stats.
Identities = 34/66 (51%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 115 TKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKH 174
T +KP N V+ + +IH+ K L K F KRAP AIK +R+FV K M T+D RID LN
Sbjct: 77 TGRKPDNIVM--EASIHLSKLLKKRTFHKRAPIAIKRIRSFVGKLMKTKDNRIDASLNTF 134
Query: 175 IWSKGI 180
IW KG+
Sbjct: 135 IWHKGV 140
>pdb|3J21|AA Chain a, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 95
Score = 45.8 bits (107), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/38 (50%), Positives = 27/38 (71%)
Query: 143 KRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
KRAPRA+K VR FV + ++V ID ++N+ IW +GI
Sbjct: 26 KRAPRAVKFVREFVARHAKAQEVIIDPKVNEKIWERGI 63
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 33.1 bits (74), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 13/48 (27%)
Query: 604 QYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQR 651
+YSVVYPT + + Q +GR IR D GA +++D+R
Sbjct: 550 EYSVVYPTAI-------------KIRQEIGRLIRSAEDTGACVILDKR 584
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 38 KAKNCLLESPTGSGKTLALLCSVLAWQRKEK 68
K+ LESPTGSGKT+ L S L + + K
Sbjct: 21 KSYGVALESPTGSGKTIMALKSALQYSSERK 51
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 290 KAKNCLLESPTGSGKTLALLCSVLAWQRKEK 320
K+ LESPTGSGKT+ L S L + + K
Sbjct: 21 KSYGVALESPTGSGKTIMALKSALQYSSERK 51
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 13/48 (27%)
Query: 604 QYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQR 651
+YSVVYPT + + Q +GR IR D GA +++D+R
Sbjct: 532 EYSVVYPTAI-------------KIRQEIGRLIRSAEDTGACVILDKR 566
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 38 KAKNCLLESPTGSGKTLALLCSVLAWQRKEK 68
K+ LESPTGSGKT+ L S L + + K
Sbjct: 3 KSYGVALESPTGSGKTIMALKSALQYSSERK 33
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 290 KAKNCLLESPTGSGKTLALLCSVLAWQRKEK 320
K+ LESPTGSGKT+ L S L + + K
Sbjct: 3 KSYGVALESPTGSGKTIMALKSALQYSSERK 33
>pdb|4I4T|F Chain F, Crystal Structure Of Tubulin-rb3-ttl-zampanolide Complex
pdb|4I50|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-epothilone A
Complex
pdb|4I55|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl Complex
pdb|4IIJ|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-apo Complex
pdb|4IHJ|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-adp Complex
Length = 384
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 506 CIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTP-CIEDL 552
CIE ST+ L FQL D M+DE L ++++V P C + L
Sbjct: 297 CIEP--AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKL 342
>pdb|2WFM|A Chain A, Crystal Structure Of Polyneuridine Aldehyde Esterase
Mutant (H244a)
pdb|2WFM|B Chain B, Crystal Structure Of Polyneuridine Aldehyde Esterase
Mutant (H244a)
pdb|2WFM|C Chain C, Crystal Structure Of Polyneuridine Aldehyde Esterase
Mutant (H244a)
pdb|2WFM|D Chain D, Crystal Structure Of Polyneuridine Aldehyde Esterase
Mutant (H244a)
pdb|2WFM|E Chain E, Crystal Structure Of Polyneuridine Aldehyde Esterase
Mutant (H244a)
Length = 264
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 237 YTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKY 274
++ GG+ + ++ YP +IS+ +S + PNH L Y
Sbjct: 86 HSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTY 123
>pdb|2WFL|B Chain B, Crystal Structure Of Polyneuridine Aldehyde Esterase
Length = 264
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 237 YTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKY 274
++ GG+ + ++ YP +IS+ +S + PNH L Y
Sbjct: 86 HSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTY 123
>pdb|2WFL|A Chain A, Crystal Structure Of Polyneuridine Aldehyde Esterase
Length = 264
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 237 YTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKY 274
++ GG+ + ++ YP +IS+ +S + PNH L Y
Sbjct: 86 HSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTY 123
>pdb|3GZJ|A Chain A, Crystal Structure Of Polyneuridine Aldehyde Esterase
Complexed With 16-Epi-Vellosimine
pdb|3GZJ|B Chain B, Crystal Structure Of Polyneuridine Aldehyde Esterase
Complexed With 16-Epi-Vellosimine
pdb|3GZJ|C Chain C, Crystal Structure Of Polyneuridine Aldehyde Esterase
Complexed With 16-Epi-Vellosimine
pdb|3GZJ|D Chain D, Crystal Structure Of Polyneuridine Aldehyde Esterase
Complexed With 16-Epi-Vellosimine
pdb|3GZJ|E Chain E, Crystal Structure Of Polyneuridine Aldehyde Esterase
Complexed With 16-Epi-Vellosimine
Length = 258
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 237 YTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKY 274
++ GG+ + ++ YP +IS+ +S + PNH L Y
Sbjct: 80 HSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTY 117
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
0.321 0.135 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,598,826
Number of Sequences: 62578
Number of extensions: 784097
Number of successful extensions: 1794
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1768
Number of HSP's gapped (non-prelim): 29
length of query: 795
length of database: 14,973,337
effective HSP length: 107
effective length of query: 688
effective length of database: 8,277,491
effective search space: 5694913808
effective search space used: 5694913808
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)