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= 032770
(134 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|U Chain U, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 138
Score = 217 bits (552), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 104/126 (82%), Positives = 119/126 (94%), Gaps = 4/126 (3%)
Query: 1 MAD----KAITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANA 56
MAD A+T+RTRKFMTNRLLSRKQFV++VLHPGRANVSKA+LKEKLA++Y+V+D+N
Sbjct: 1 MADTKTAPAVTLRTRKFMTNRLLSRKQFVLEVLHPGRANVSKADLKEKLAKLYEVKDSNC 60
Query: 57 IFVFKFRTHFGGGKSTGFGLIYDSVESAKKFEPKYRLIRNGLATKVEKSRKQMKERKNRQ 116
IFVFKFRTHFGGGKSTGFGLIYD++++AKK+EPKYRLIRNGLATKVEKSRKQMKERKNR
Sbjct: 61 IFVFKFRTHFGGGKSTGFGLIYDNLDAAKKYEPKYRLIRNGLATKVEKSRKQMKERKNRA 120
Query: 117 KKIRGV 122
KKIRGV
Sbjct: 121 KKIRGV 126
>pdb|3IZB|U Chain U, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5C|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
pdb|3J16|D Chain D, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 135
Score = 158 bits (399), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 82/122 (67%), Positives = 99/122 (81%), Gaps = 3/122 (2%)
Query: 1 MADKAITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVF 60
M+D A+TIRTRK ++N LL+RKQFV+DVLHP RANVSK EL+EKLA +Y + +A+ VF
Sbjct: 1 MSD-AVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKA-EKDAVSVF 58
Query: 61 KFRTHFGGGKSTGFGLIYDSVESAKKFEPKYRLIRNGLATKVEK-SRKQMKERKNRQKKI 119
FRT FGGGKS GFGL+Y+SV AKKFEP YRL+R GLA KVEK SR+Q K++KNR KKI
Sbjct: 59 GFRTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYGLAEKVEKASRQQRKQKKNRDKKI 118
Query: 120 RG 121
G
Sbjct: 119 FG 120
>pdb|2XZM|P Chain P, 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|P Chain P, 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 = 149
Score = 99.0 bits (245), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 50/117 (42%), Positives = 73/117 (62%), Gaps = 1/117 (0%)
Query: 5 AITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRT 64
I IRT+K + N LLSR+Q +DVLHP SK +++E+LA+ V DA + V+ F T
Sbjct: 2 TIVIRTKKILVNPLLSRRQLSLDVLHPDSPTASKEKIREELAKQLKV-DARNVVVYGFST 60
Query: 65 HFGGGKSTGFGLIYDSVESAKKFEPKYRLIRNGLATKVEKSRKQMKERKNRQKKIRG 121
+GGGKSTGF L+YD+ + K+EP YRL + + + +R+ KE K + K+ G
Sbjct: 61 QYGGGKSTGFALVYDNQQYLLKYEPNYRLRKVKILGEKPNTRRSFKELKRKIKRTSG 117
>pdb|3ZEY|T Chain T, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 137
Score = 90.9 bits (224), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 62/117 (52%), Positives = 82/117 (70%), Gaps = 1/117 (0%)
Query: 6 ITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAEL-KEKLARMYDVRDANAIFVFKFRT 64
+T+RT +F N+LL+RKQFV++V HPG A+L + +LA +Y V D N I VF F+T
Sbjct: 10 VTVRTSQFKVNKLLNRKQFVVEVNHPGWCGTVPAKLIRNRLASLYKVADENQISVFGFKT 69
Query: 65 HFGGGKSTGFGLIYDSVESAKKFEPKYRLIRNGLATKVEKSRKQMKERKNRQKKIRG 121
FGGGK+TGFGLIYD + + K+ EP YR R G+ K +RK +KER+NR KKIRG
Sbjct: 70 KFGGGKTTGFGLIYDDLAAMKRIEPNYRKARLGMGKKKLPARKSVKERRNRNKKIRG 126
>pdb|3J20|V Chain V, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
pdb|3J21|6 Chain 6, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 99
Score = 66.2 bits (160), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 34/98 (34%), Positives = 53/98 (54%), Gaps = 1/98 (1%)
Query: 6 ITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTH 65
+ IR ++ N+L+ RK+ ++ HPG S+ ++K KL M D+ + + R++
Sbjct: 1 MEIRIKEIKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQY-IRSY 59
Query: 66 FGGGKSTGFGLIYDSVESAKKFEPKYRLIRNGLATKVE 103
FG S G+ YDS E EP+Y LIR+GL K E
Sbjct: 60 FGSYISKGYAKAYDSKERMLYIEPEYILIRDGLIEKKE 97
>pdb|2V94|A Chain A, Crystal Structure Of P. Abyssi Rps24
pdb|2V94|B Chain B, Crystal Structure Of P. Abyssi Rps24
Length = 107
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 49/96 (51%), Gaps = 1/96 (1%)
Query: 8 IRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFG 67
I+ + N+L+ RK+ ++ HPG S+ ++K KL D+ + + R++FG
Sbjct: 11 IKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAXLDLNPETTVIQY-IRSYFG 69
Query: 68 GGKSTGFGLIYDSVESAKKFEPKYRLIRNGLATKVE 103
KS G+ Y + EP+Y LIR+G+ K E
Sbjct: 70 SYKSKGYAKYYYDKDRXLYIEPEYILIRDGIIEKKE 105
>pdb|2G1D|A Chain A, Solution Structure Of Ribosomal Protein S24e From
Thermoplasma Acidophilum
Length = 98
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 16 NRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFG 75
N +L RK+ + S+ E+KE +A+ V D + V + G + G+
Sbjct: 11 NPILKRKEIKYVLKFDSSRTPSREEIKELIAKHEGV-DKELVIVDNNKQLTGKHEIEGYT 69
Query: 76 LIYDSVESAKKFEPKYRLIRNGLATK 101
IY SA +EP Y LIRNGL K
Sbjct: 70 KIYADKPSAMLYEPDYELIRNGLKQK 95
>pdb|1XN9|A Chain A, Solution Structure Of Methanosarcina Mazei Protein
Rps24e: The Northeast Structural Genomics Consortium
Target Mar11
Length = 101
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 49/94 (52%), Gaps = 2/94 (2%)
Query: 6 ITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTH 65
+ I+ K N LL+R++ V + G + S+ +++ KLA M + + + + +T
Sbjct: 1 MDIKIIKDKKNPLLNRRELDFIVKYEG-STPSRNDVRNKLAAMLNA-PLELLVIQRIKTE 58
Query: 66 FGGGKSTGFGLIYDSVESAKKFEPKYRLIRNGLA 99
+G +S G+ +Y+ + K+ E +Y L RN +
Sbjct: 59 YGMQESKGYAKLYEDADRMKQVEQEYVLKRNAVP 92
>pdb|4BAA|A Chain A, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|B Chain B, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|C Chain C, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|D Chain D, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
Length = 705
Score = 28.1 bits (61), Expect = 1.7, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 86 KFEPKYRLIRNGLATKVEKSRKQMKERKNRQK 117
KF P YR +R L T V +R++ +++ QK
Sbjct: 642 KFLPFYRFVREELDTGVMSARREQTPQEDVQK 673
>pdb|2YII|A Chain A, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|B Chain B, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|C Chain C, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|D Chain D, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|4BAB|A Chain A, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|B Chain B, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|C Chain C, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|D Chain D, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
Length = 705
Score = 28.1 bits (61), Expect = 1.7, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 86 KFEPKYRLIRNGLATKVEKSRKQMKERKNRQK 117
KF P YR +R L T V +R++ +++ QK
Sbjct: 642 KFLPFYRFVREELDTGVMSARREQTPQEDVQK 673
>pdb|1QDL|A Chain A, The Crystal Structure Of Anthranilate Synthase From
Sulfolobus Solfataricus
Length = 422
Score = 27.3 bits (59), Expect = 2.6, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 53 DANAIFVFKFRTHFGGGK----STGFGLIYDSVESAKKFEPKYRL 93
D NA F RT F + G G++YDS ++ FE +++L
Sbjct: 368 DGNAEFAIAIRTAFLNKELLRIHAGAGIVYDSNPESEYFETEHKL 412
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
0.322 0.136 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,093,759
Number of Sequences: 62578
Number of extensions: 112978
Number of successful extensions: 413
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 397
Number of HSP's gapped (non-prelim): 26
length of query: 134
length of database: 14,973,337
effective HSP length: 88
effective length of query: 46
effective length of database: 9,466,473
effective search space: 435457758
effective search space used: 435457758
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: 46 (22.3 bits)