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= psy397
(202 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 = 128 bits (321), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 60/99 (60%), Positives = 79/99 (79%), Gaps = 1/99 (1%)
Query: 1 MKTVLSASTVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPEN- 59
M +A VT++TRK+MTNRLL RKQ V++VLHPG+ +V K D++EKL+K+++ K N
Sbjct: 1 MADTKTAPAVTLRTRKFMTNRLLSRKQFVLEVLHPGRANVSKADLKEKLAKLYEVKDSNC 60
Query: 60 IFAFGFQTNFGGGKSTGFALIYDSIDLAKKFEPKYRLQR 98
IF F F+T+FGGGKSTGF LIYD++D AKK+EPKYRL R
Sbjct: 61 IFVFKFRTHFGGGKSTGFGLIYDNLDAAKKYEPKYRLIR 99
>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 = 114 bits (284), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 55/125 (44%), Positives = 82/125 (65%), Gaps = 7/125 (5%)
Query: 7 ASTVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQ 66
+ VTI+TRK ++N LL RKQ VVDVLHP + +V K ++REKL++++K++ + + FGF+
Sbjct: 2 SDAVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKAEKDAVSVFGFR 61
Query: 67 TNFGGGKSTGFALIYDSIDLAKKFEPKYRLQRVSTKSLLVLIIATIGITSCQEAEHKIDH 126
T FGGGKS GF L+Y+S+ AKKFEP YRL R + + S Q+ + K +
Sbjct: 62 TQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYG-------LAEKVEKASRQQRKQKKNR 114
Query: 127 SELVF 131
+ +F
Sbjct: 115 DKKIF 119
>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 = 102 bits (254), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 45/91 (49%), Positives = 63/91 (69%)
Query: 9 TVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTN 68
T+ I+T+K + N LL R+Q+ +DVLHP P+ K IRE+L+K K N+ +GF T
Sbjct: 2 TIVIRTKKILVNPLLSRRQLSLDVLHPDSPTASKEKIREELAKQLKVDARNVVVYGFSTQ 61
Query: 69 FGGGKSTGFALIYDSIDLAKKFEPKYRLQRV 99
+GGGKSTGFAL+YD+ K+EP YRL++V
Sbjct: 62 YGGGKSTGFALVYDNQQYLLKYEPNYRLRKV 92
>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 = 57.0 bits (136), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 49/89 (55%)
Query: 10 VTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNF 69
+ I+ ++ N+L+GRK++ ++ HPG+P+ + D++ KL M PE ++ F
Sbjct: 1 MEIRIKEIKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYF 60
Query: 70 GGGKSTGFALIYDSIDLAKKFEPKYRLQR 98
G S G+A YDS + EP+Y L R
Sbjct: 61 GSYISKGYAKAYDSKERMLYIEPEYILIR 89
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 45/87 (51%)
Query: 12 IKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGG 71
IK + N+L+GRK++ ++ HPG+P+ + D++ KL PE ++ FG
Sbjct: 11 IKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAXLDLNPETTVIQYIRSYFGS 70
Query: 72 GKSTGFALIYDSIDLAKKFEPKYRLQR 98
KS G+A Y D EP+Y L R
Sbjct: 71 YKSKGYAKYYYDKDRXLYIEPEYILIR 97
>pdb|3ZEY|T Chain T, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 137
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 45/95 (47%), Positives = 62/95 (65%), Gaps = 2/95 (2%)
Query: 8 STVTIKTRKYMTNRLLGRKQMVVDVLHPG-KPSVKKTDIREKLSKMFKSKPEN-IFAFGF 65
+ VT++T ++ N+LL RKQ VV+V HPG +V IR +L+ ++K EN I FGF
Sbjct: 8 AEVTVRTSQFKVNKLLNRKQFVVEVNHPGWCGTVPAKLIRNRLASLYKVADENQISVFGF 67
Query: 66 QTNFGGGKSTGFALIYDSIDLAKKFEPKYRLQRVS 100
+T FGGGK+TGF LIYD + K+ EP YR R+
Sbjct: 68 KTKFGGGKTTGFGLIYDDLAAMKRIEPNYRKARLG 102
>pdb|1XN9|A Chain A, Solution Structure Of Methanosarcina Mazei Protein
Rps24e: The Northeast Structural Genomics Consortium
Target Mar11
Length = 101
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 48/90 (53%), Gaps = 3/90 (3%)
Query: 10 VTIKTRKYMTNRLLGRKQMVVDVLHPGK-PSVKKTDIREKLSKMFKSKPENIFAFGFQTN 68
+ IK K N LL R+++ V + G PS + D+R KL+ M + E + +T
Sbjct: 1 MDIKIIKDKKNPLLNRRELDFIVKYEGSTPS--RNDVRNKLAAMLNAPLELLVIQRIKTE 58
Query: 69 FGGGKSTGFALIYDSIDLAKKFEPKYRLQR 98
+G +S G+A +Y+ D K+ E +Y L+R
Sbjct: 59 YGMQESKGYAKLYEDADRMKQVEQEYVLKR 88
>pdb|2CTZ|A Chain A, Crystal Structure Of O-Acetyl Homoserine Sulfhydrylase
From Thermus Thermophilus Hb8
pdb|2CTZ|B Chain B, Crystal Structure Of O-Acetyl Homoserine Sulfhydrylase
From Thermus Thermophilus Hb8
Length = 421
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 4 VLSASTVTIKTRKYMTNRL-----LGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPE 58
+L T++++ +++ N L L + V V +PG P D + K FK KP
Sbjct: 281 LLGMETLSLRAERHVENTLHLAHWLLEQPQVAWVNYPGLPHHPHHD---RAQKYFKGKPG 337
Query: 59 NIFAFGFQTNFGGGK 73
+ FG + + K
Sbjct: 338 AVLTFGLKGGYEAAK 352
>pdb|2KVK|A Chain A, Solution Structure Of AdfCOFILIN (LDCOF) FROM LEISHMANIA
DONOVANI
Length = 144
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 23 LGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALI 80
+G ++V G+ SV TD++EK F ++ AF F+ N G K LI
Sbjct: 31 IGADGKKIEVTEVGERSVNYTDLKEK----FSTEKPCYVAFDFEYNDAGSKREKLILI 84
>pdb|1Z5V|A Chain A, Crystal Structure Of Human Gamma-Tubulin Bound To
Gtpgammas
pdb|1Z5W|A Chain A, Crystal Structure Of Gamma-Tubulin Bound To Gtp
Length = 474
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 1 MKTVLSASTVTIKTRKYMTNRLLG 24
+ T++SAST T++ YM N L+G
Sbjct: 232 VSTIMSASTTTLRYPGYMNNDLIG 255
>pdb|3CB2|A Chain A, Crystal Structure Of Human Gamma-Tubulin Bound To Gdp
pdb|3CB2|B Chain B, Crystal Structure Of Human Gamma-Tubulin Bound To Gdp
Length = 475
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 1 MKTVLSASTVTIKTRKYMTNRLLG 24
+ T++SAST T++ YM N L+G
Sbjct: 232 VSTIMSASTTTLRYPGYMNNDLIG 255
>pdb|2K5H|A Chain A, Solution Nmr Structure Of Protein Encoded By Mth693 From
Methanobacterium Thermoautotrophicum: Northeast
Structural Genomics Consortium Target Tt824a
Length = 101
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 21/31 (67%)
Query: 14 TRKYMTNRLLGRKQMVVDVLHPGKPSVKKTD 44
++K +++RL+GRK +V++ + P + K D
Sbjct: 32 SKKAVSDRLIGRKGVVMEAISPQNSGLVKVD 62
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: 5,467,101
Number of Sequences: 62578
Number of extensions: 205592
Number of successful extensions: 437
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 425
Number of HSP's gapped (non-prelim): 13
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
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: 49 (23.5 bits)