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= 027050
(229 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FRT|A Chain A, The Structure Of Human Chmp3 (Residues 8 - 222).
pdb|3FRT|B Chain B, The Structure Of Human Chmp3 (Residues 8 - 222)
Length = 218
Score = 150 bits (380), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 76/176 (43%), Positives = 113/176 (64%), Gaps = 1/176 (0%)
Query: 11 KPNPQQLLRDWQRKLRQECRNIERQIRDIQREEKNVQKAIKDAAKRNDLSSAKSLAQELV 70
KP P++L+ +W K+R+E R ++RQIRDIQREE+ V++++KDAAK+ LA+E++
Sbjct: 6 KP-PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMI 64
Query: 71 RSRKTVNRLYENKAQMNSISMHLGESVAIARTVGHLNKSAEVMKLVNNLMKAPEVAATMQ 130
RSRK V++LY +KA MNS+ M + +A+ R G L KS EVMK + +L+K PE+ ATM+
Sbjct: 65 RSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMR 124
Query: 131 EFSKEMTKAGVIEEFVNDAVDTALDSXXXXXXXXXXVDKVLTAIAGETAAQLPEAV 186
E SKEM KAG+IEE + D ++ D +D++L I + P V
Sbjct: 125 ELSKEMMKAGIIEEMLEDTFESMDDQEEMEEEAEMEIDRILFEITAGALGKAPSKV 180
>pdb|3FRV|A Chain A, Structure Of Human Chmp3 (Residues 1-150)
Length = 152
Score = 145 bits (365), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 70/142 (49%), Positives = 103/142 (72%), Gaps = 1/142 (0%)
Query: 11 KPNPQQLLRDWQRKLRQECRNIERQIRDIQREEKNVQKAIKDAAKRNDLSSAKSLAQELV 70
KP P++L+ +W K+R+E R ++RQIRDIQREE+ V++++KDAAK+ LA+E++
Sbjct: 12 KP-PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMI 70
Query: 71 RSRKTVNRLYENKAQMNSISMHLGESVAIARTVGHLNKSAEVMKLVNNLMKAPEVAATMQ 130
RSRK V++LY +KA MNS+ M + +A+ R G L KS EVMK + +L+K PE+ ATM+
Sbjct: 71 RSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMR 130
Query: 131 EFSKEMTKAGVIEEFVNDAVDT 152
E SKEM KAG+IEE + D ++
Sbjct: 131 ELSKEMMKAGIIEEMLEDTFES 152
>pdb|2GD5|A Chain A, Structural Basis For Budding By The Escrtiii Factor Chmp3
pdb|2GD5|B Chain B, Structural Basis For Budding By The Escrtiii Factor Chmp3
pdb|2GD5|C Chain C, Structural Basis For Budding By The Escrtiii Factor Chmp3
pdb|2GD5|D Chain D, Structural Basis For Budding By The Escrtiii Factor Chmp3
Length = 179
Score = 132 bits (333), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 72/173 (41%), Positives = 106/173 (61%), Gaps = 1/173 (0%)
Query: 11 KPNPQQLLRDWQRKLRQECRNIERQIRDIQREEKNVQKAIKDAAKRNDLSSAKSLAQELV 70
KP P++L+ +W K+R+E R ++RQIRDIQREE+ V++++KDAAK+ LA+E +
Sbjct: 6 KP-PKELVNEWSLKIRKEXRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEXI 64
Query: 71 RSRKTVNRLYENKAQMNSISMHLGESVAIARTVGHLNKSAEVMKLVNNLMKAPEVAATMQ 130
RSRK V++LY +KA NS+ +A+ R G L KS EV K +L+K PE+ AT +
Sbjct: 65 RSRKAVSKLYASKAHXNSVLXGXKNQLAVLRVAGSLQKSTEVXKAXQSLVKIPEIQATXR 124
Query: 131 EFSKEMTKAGVIEEFVNDAVDTALDSXXXXXXXXXXVDKVLTAIAGETAAQLP 183
E SKE KAG+IEE + D ++ D +D++L I + P
Sbjct: 125 ELSKEXXKAGIIEEMLEDTFESMDDQEEXEEEAEXEIDRILFEITAGALGKAP 177
>pdb|3C5Y|A Chain A, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|B Chain B, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|C Chain C, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|D Chain D, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|E Chain E, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|F Chain F, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|G Chain G, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|H Chain H, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|I Chain I, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|J Chain J, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|K Chain K, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|L Chain L, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|M Chain M, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|N Chain N, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|O Chain O, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
pdb|3C5Y|P Chain P, Crystal Structure Of A Putative Ribose 5-Phosphate
Isomerase (Saro_3514) From Novosphingobium
Aromaticivorans Dsm At 1.81 A Resolution
Length = 231
Score = 30.4 bits (67), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 18 LRDWQRKLRQECRNI--ERQIRDIQREEKNVQKAIKDAAKRNDLSSAKSLAQELVRS 72
L+D RKL R + R+ +I R+ + + + +KDA+ R+ L+ K++ Q+L+R+
Sbjct: 146 LQDVYRKLFDGERGLGYPRERAEIXRKNRGILRELKDASCRDXLTVLKTVDQDLLRA 202
>pdb|2ZTM|A Chain A, T190s Mutant Of D-3-Hydroxybutyrate Dehydrogenase
pdb|2ZTM|B Chain B, T190s Mutant Of D-3-Hydroxybutyrate Dehydrogenase
pdb|2ZTM|C Chain C, T190s Mutant Of D-3-Hydroxybutyrate Dehydrogenase
pdb|2ZTM|D Chain D, T190s Mutant Of D-3-Hydroxybutyrate Dehydrogenase
Length = 260
Score = 30.0 bits (66), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 197 TSRAAQEEDAVAEGIDDEKELEEIRARLA 225
T+ AAQ D V G D E+E++RA LA
Sbjct: 22 TALAAQGADIVLNGFGDAAEIEKVRAGLA 50
>pdb|1WMB|A Chain A, Crystal Structure Of Nad Dependent D-3-Hydroxybutylate
Dehydrogenase
pdb|1WMB|B Chain B, Crystal Structure Of Nad Dependent D-3-Hydroxybutylate
Dehydrogenase
pdb|1X1T|A Chain A, Crystal Structure Of D-3-hydroxybutyrate Dehydrogenase
From Pseudomonas Fragi Complexed With Nad+
pdb|2ZTL|A Chain A, Closed Conformation Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+ And L-3-Hydroxybutyrate
pdb|2ZTL|B Chain B, Closed Conformation Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+ And L-3-Hydroxybutyrate
pdb|2ZTL|C Chain C, Closed Conformation Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+ And L-3-Hydroxybutyrate
pdb|2ZTL|D Chain D, Closed Conformation Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+ And L-3-Hydroxybutyrate
pdb|2ZTV|A Chain A, The Binary Complex Of D-3-Hydroxybutyrate Dehydrogenase
With Nad+
pdb|2ZTV|B Chain B, The Binary Complex Of D-3-Hydroxybutyrate Dehydrogenase
With Nad+
pdb|2ZTV|C Chain C, The Binary Complex Of D-3-Hydroxybutyrate Dehydrogenase
With Nad+
pdb|2ZTV|D Chain D, The Binary Complex Of D-3-Hydroxybutyrate Dehydrogenase
With Nad+
Length = 260
Score = 30.0 bits (66), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 197 TSRAAQEEDAVAEGIDDEKELEEIRARLA 225
T+ AAQ D V G D E+E++RA LA
Sbjct: 22 TALAAQGADIVLNGFGDAAEIEKVRAGLA 50
>pdb|2ZTU|A Chain A, T190a Mutant Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+
pdb|2ZTU|B Chain B, T190a Mutant Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+
pdb|2ZTU|C Chain C, T190a Mutant Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+
pdb|2ZTU|D Chain D, T190a Mutant Of D-3-Hydroxybutyrate Dehydrogenase
Complexed With Nad+
Length = 260
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 197 TSRAAQEEDAVAEGIDDEKELEEIRARLA 225
T+ AAQ D V G D E+E++RA LA
Sbjct: 22 TALAAQGADIVLNGFGDAAEIEKVRAGLA 50
>pdb|3ECQ|A Chain A, Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus
Pneumoniae: Semet Structure
pdb|3ECQ|B Chain B, Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus
Pneumoniae: Semet Structure
Length = 1531
Score = 27.7 bits (60), Expect = 5.7, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 178 TAAQLPEAVRKERVKQSAQTSRAAQEEDAVAEGI------DDEKELEEIRARLAKVRS 229
T L E K + A T+ + DA+ E + DD+ +EE RA +AK+ +
Sbjct: 1385 TGKXLTENALKNYLPTVAXTNYTKESXDALKEAVFNLSQADDDISVEEARAEIAKIEA 1442
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 29/45 (64%), Gaps = 3/45 (6%)
Query: 36 IRDIQREE---KNVQKAIKDAAKRNDLSSAKSLAQELVRSRKTVN 77
I DI ++E K +++ ++D + ND +A+ ++QE R R+TV+
Sbjct: 16 IFDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVD 60
>pdb|3F1E|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400
Length = 378
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 36 IRDIQREE---KNVQKAIKDAAKRNDLSSAKSLAQELVRSRKTVNRL 79
I DI ++E K +++ ++D + ND +A+ ++QE R R+TV+
Sbjct: 29 IFDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTF 75
>pdb|2B9M|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor
Rf2 From A Crystal Structure Of The Whole Ribosomal
Complex. This File Contains The 30s Ribosomal Subunit,
Trnas, Mrna And Release Factor Rf2 From A Crystal
Structure Of The Whole Ribosomal Complex". The Entire
Crystal Structure Contains One 70s Ribosome, Trnas,
Mrna And Release Factor Rf2 And Is Described In Remark
400
Length = 365
Score = 26.9 bits (58), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 34 RQIRDIQREE---KNVQKAIKDAAKRNDLSSAKSLAQELVRSRKTVN 77
R DI ++E K +++ ++D + ND +A+ ++QE R R+TV+
Sbjct: 14 RGYLDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVD 60
>pdb|2WH1|Y Chain Y, Insights Into Translational Termination From The
Structure Of Rf2 Bound To The Ribosome
pdb|2WH3|Y Chain Y, Insights Into Translational Termination From The
Structure Of Rf2 Bound To The Ribosome). This File
Contains The 30s Subunit
Length = 351
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 34 RQIRDIQREE---KNVQKAIKDAAKRNDLSSAKSLAQELVRSRKTVN 77
R DI ++E K +++ ++D + ND +A+ ++QE R R+TV+
Sbjct: 9 RGYLDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVD 55
>pdb|2X9R|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
Length = 351
Score = 26.9 bits (58), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 34 RQIRDIQREE---KNVQKAIKDAAKRNDLSSAKSLAQELVRSRKTVN 77
R DI ++E K +++ ++D + ND +A+ ++QE R R+TV+
Sbjct: 9 RGYLDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVD 55
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
0.310 0.123 0.316
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,886,482
Number of Sequences: 62578
Number of extensions: 148012
Number of successful extensions: 484
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 466
Number of HSP's gapped (non-prelim): 28
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)