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= 032415
(141 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|Q Chain Q, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 141
Score = 203 bits (516), Expect = 3e-53, Method: Compositional matrix adjust.
Identities = 95/124 (76%), Positives = 116/124 (93%)
Query: 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKR 60
MGRVRTKTVKK+SRQVIE+YYSRMTLDFHTNKK+LEEV+I+PSKRLRNK+AGF+THLM+R
Sbjct: 1 MGRVRTKTVKKTSRQVIEKYYSRMTLDFHTNKKVLEEVSILPSKRLRNKVAGFTTHLMRR 60
Query: 61 IQKGPVRGISLKLQEEERERRMDFVPDESAIKTDQIEVDKETLDMLEALGMNEIPGLVRV 120
IQ+GPVRGISLKLQEEERERRMDFVP++SA++ ++I VDKET++ML ALGM ++PG+ R
Sbjct: 61 IQRGPVRGISLKLQEEERERRMDFVPEKSALEVEEIRVDKETMEMLAALGMADLPGVERQ 120
Query: 121 DPVA 124
V+
Sbjct: 121 QEVS 124
>pdb|2XZM|V Chain V, 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|V Chain V, 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 = 130
Score = 177 bits (448), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 83/124 (66%), Positives = 103/124 (83%)
Query: 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKR 60
MGRVRTKTVK++++ +IE YYS++T DFH NKKIL EVA +PSKRLRNKIAGF+THLMKR
Sbjct: 1 MGRVRTKTVKRAAKSLIEHYYSKLTNDFHFNKKILSEVAQVPSKRLRNKIAGFATHLMKR 60
Query: 61 IQKGPVRGISLKLQEEERERRMDFVPDESAIKTDQIEVDKETLDMLEALGMNEIPGLVRV 120
IQKGPVRGISLK+QEEERERR+D+VP++S I +++ +D ET +ML+ LG IPGLV
Sbjct: 61 IQKGPVRGISLKVQEEERERRLDYVPEKSIIDIEKVTIDNETKEMLKKLGYQNIPGLVSA 120
Query: 121 DPVA 124
A
Sbjct: 121 SAPA 124
>pdb|3IZB|Q Chain Q, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|K Chain K, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|K Chain K, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|R Chain R, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|R Chain R, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 136
Score = 151 bits (381), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 71/115 (61%), Positives = 95/115 (82%), Gaps = 4/115 (3%)
Query: 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKR 60
MGRVRTKTVK++S+ +IERYY ++TLDF TNK++ +E+A I SKRLRNKIAG++THLMKR
Sbjct: 1 MGRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKR 60
Query: 61 IQKGPVRGISLKLQEEERERRMDFVPDESAIKTDQ----IEVDKETLDMLEALGM 111
IQKGPVRGIS KLQEEERER+ +VP+ SA+ + + VD +T D++++LG+
Sbjct: 61 IQKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVLNVDNQTSDLVKSLGL 115
>pdb|3ZEY|L Chain L, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 142
Score = 140 bits (353), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 65/112 (58%), Positives = 93/112 (83%), Gaps = 3/112 (2%)
Query: 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKR 60
MG++RTKTVK++S+Q++E+Y+S++ DF+ NK+I+ +V I SK+L+NKIAG++TH+MKR
Sbjct: 1 MGKIRTKTVKRASKQIVEKYFSKLNKDFYQNKRIVMDVTIARSKKLKNKIAGYATHIMKR 60
Query: 61 IQKGPVRGISLKLQEEERERRMDFVPDESAIK---TDQIEVDKETLDMLEAL 109
+ +GPVRGISLKLQEEERERRMD+VP+ S + D I VDK+TL ML+ +
Sbjct: 61 LARGPVRGISLKLQEEERERRMDYVPEVSHVDQAIQDGIRVDKQTLAMLKRM 112
>pdb|1RQ6|A Chain A, Solution Structure Of Ribosomal Protein S17e From
Methanobacterium Thermoautotrophicum, Northeast
Structural Genomics Consortium Target Tt802 ONTARIO
CENTER FOR Structural Proteomics Target Mth0803
Length = 62
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 43/60 (71%)
Query: 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKR 60
MG +RT VK+ ++++IE + + T DF TNKK++EE + + +K LRNKIAG+ T ++ +
Sbjct: 1 MGNIRTSFVKRIAKEMIETHPGKFTDDFDTNKKLVEEFSTVSTKHLRNKIAGYITRIISQ 60
>pdb|3J20|S Chain S, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 67
Score = 53.1 bits (126), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 45/66 (68%)
Query: 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKR 60
MG++R +K+ +R+++ +Y + T DF NKK ++E+ + SK++RN+IAG+ T L++
Sbjct: 1 MGKIRQGFIKRVARELVNKYPNEFTTDFEHNKKKVQELTNVTSKKIRNRIAGYVTKLVRM 60
Query: 61 IQKGPV 66
+G +
Sbjct: 61 KMEGKI 66
>pdb|2G6X|A Chain A, Crystal Structure Of A Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
pdb|2G6X|B Chain B, Crystal Structure Of A Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
pdb|2G6X|C Chain C, Crystal Structure Of A Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
pdb|2G6X|D Chain D, Crystal Structure Of A Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
pdb|2G6Y|A Chain A, Crystal Structure Of The Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
pdb|2G6Y|B Chain B, Crystal Structure Of The Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
pdb|2G6Y|C Chain C, Crystal Structure Of The Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
pdb|2G6Y|D Chain D, Crystal Structure Of The Novel Green Fluorescent Protein
From Marine Copepod Pontellina Plumata
Length = 217
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 51 AGFSTHLMKRIQKGPVRGISLKLQEEERERRMDF------VPDESAIKTDQIEVDKETLD 104
G++ +++ + G V +S + E DF P++S I TD+I T++
Sbjct: 79 GGYTNTRIEKYEDGGVLHVSFSYRYEAGRVIGDFKVMGTGFPEDSVIFTDKIIRSNATVE 138
Query: 105 MLEALGMNEIPG 116
L +G N++ G
Sbjct: 139 HLHPMGDNDLDG 150
>pdb|2G3O|A Chain A, The 2.1a Crystal Structure Of Copgfp
pdb|2G3O|B Chain B, The 2.1a Crystal Structure Of Copgfp
pdb|2G3O|C Chain C, The 2.1a Crystal Structure Of Copgfp
pdb|2G3O|D Chain D, The 2.1a Crystal Structure Of Copgfp
pdb|2G3O|E Chain E, The 2.1a Crystal Structure Of Copgfp
pdb|2G3O|F Chain F, The 2.1a Crystal Structure Of Copgfp
Length = 220
Score = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 51 AGFSTHLMKRIQKGPVRGISLKLQEEERERRMDF------VPDESAIKTDQIEVDKETLD 104
G++ +++ + G V +S + E DF P++S I TD+I T++
Sbjct: 79 GGYTNTRIEKYEDGGVLHVSFSYRYEAGRVIGDFKVVGTGFPEDSVIFTDKIIRSNATVE 138
Query: 105 MLEALGMNEIPG 116
L +G N + G
Sbjct: 139 HLHPMGDNVLVG 150
>pdb|2CKF|B Chain B, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
pdb|2CKF|D Chain D, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
pdb|2CKF|F Chain F, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
Length = 174
Score = 25.8 bits (55), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 78 RERRMDFVPDESAIKTDQIEVDKETLDMLEA--LGMNEIPGLVR 119
R+RR D PD++AI D E K+ ++ L + + M + P +R
Sbjct: 57 RDRRPDPTPDDAAIYNDDFEELKQRVERLYSGQVWMEDPPSKIR 100
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 0.135 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,331,365
Number of Sequences: 62578
Number of extensions: 115249
Number of successful extensions: 239
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 231
Number of HSP's gapped (non-prelim): 13
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)