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= psy13425
(224 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U5C|H Chain H, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|H Chain H, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 190
Score = 135 bits (341), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 81/221 (36%), Positives = 120/221 (54%), Gaps = 36/221 (16%)
Query: 1 MFLANSKIIKKGGEPDAFENSISQALLELEMNS-DLKAQLRELYITRAKEIDLGGKKSVI 59
M +KI+ + P E ++QA +ELE +S +LKA+LR L +EID+ G
Sbjct: 1 MSAPQAKILSQA--PTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAG----- 53
Query: 60 VYVPMPQLKQFQKIQPRLVPKEIDLGGKKSVIVYVPMPQLKQFQKIQPRLVRELEKKFSG 119
GKK++ ++VP+P L F K+Q +L RELEKKF
Sbjct: 54 --------------------------GKKALAIFVPVPSLAGFHKVQTKLTRELEKKFQD 87
Query: 120 KHVVFIGDRKILXXXXXXXXXXXXXXXXXSRTLTSVYDCILEDIVFPAEIVGKRIKVKLD 179
+HV+F+ +R+IL SRTLT+V+D ILED+VFP EIVGKR++ +
Sbjct: 88 RHVIFLAERRILPKPSRTSRQVQKRPR--SRTLTAVHDKILEDLVFPTEIVGKRVRYLVG 145
Query: 180 GKQLIKVHLDKNQQTNIEHKTDTFSQIYKKLTGREVNFEFP 220
G ++ KV LD I++K ++F +Y KLTG+++ FE P
Sbjct: 146 GNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVFEIP 186
>pdb|3ZEY|4 Chain 4, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 202
Score = 84.3 bits (207), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 60/210 (28%), Positives = 93/210 (44%), Gaps = 34/210 (16%)
Query: 11 KGGEPDAFENSISQALLELE-MNSDLKAQLRELYITRAKEIDLGGKKSVIVYVPMPQLKQ 69
K P E S+++ L ELE + L+AQL +I +
Sbjct: 14 KRANPSQEEESVARVLFELEGSHKTLRAQLPRFHINTVRTSS------------------ 55
Query: 70 FQKIQPRLVPKEIDLGGKKSVIVYVPMPQLKQFQKIQPRLVRELEKKFSGKHVVFIGDRK 129
PR K ++I+ P+ + +KIQ L ELEK+F G VV + RK
Sbjct: 56 ----SPR--------HKKTAMIILYPLRFIMLVRKIQRTLTAELEKRFPGNIVVLVAQRK 103
Query: 130 ILXXXXXXXXXXXXXXXXXSRTLTSVYDCILEDIVFPAEIVGKRIKVKLDGKQLIKVHLD 189
I SRT +V++ IL D+++P ++VG+R + + DG +L+KV LD
Sbjct: 104 I---TKRPNDVYKLQQVQRSRTSVAVFENILNDLIYPCDVVGRRWRYRTDGSKLMKVFLD 160
Query: 190 KNQQTNIEHKTDTFSQIYKKLTGREVNFEF 219
+ +E + + +YK LT R V F F
Sbjct: 161 ARDRKRVESRLPLLAHVYKLLTHRTVTFGF 190
>pdb|2XZM|3 Chain 3, 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|3 Chain 3, 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 = 197
Score = 80.5 bits (197), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 61/204 (29%), Positives = 94/204 (46%), Gaps = 32/204 (15%)
Query: 19 ENSISQALLELE-MNSDLKAQLRELYITRAKEIDLGGKKSVIVYVPMPQLKQFQKIQPRL 77
E + AL+EL+ + DLK L + +T+ KE +
Sbjct: 16 EEQVGSALVELQNTHPDLKTSLESIILTQVKEFQIN------------------------ 51
Query: 78 VPKEIDLGGKKSVIVYVPMPQLKQFQKIQPRLVRELEKKFSGKHVVFIGDRKILXXXXXX 137
+ + K +V++YV + +L+ ELEKK + V F RKI
Sbjct: 52 ---KTNKKAKSAVLIYVHFQSYRVLLSAARKLIIELEKKL-KQIVFFTAQRKI---ESKW 104
Query: 138 XXXXXXXXXXXSRTLTSVYDCILEDIVFPAEIVGKRIKVKLDGKQLIKVHLDKNQQTNIE 197
SR LT VYD +L+D++ P+ ++GKRI+ +LDG ++ LD+N + +E
Sbjct: 105 VKEHKSQQRPRSRCLTYVYDALLDDLLLPSTLIGKRIRARLDGTSFYRIQLDQNDRDFLE 164
Query: 198 HKTDTFSQIYKKLTGREVNFEFPE 221
K D + IYK +T REV FEF E
Sbjct: 165 EKLDAITHIYKTVTTREVTFEFKE 188
>pdb|3CMM|A Chain A, Crystal Structure Of The Uba1-Ubiquitin Complex
pdb|3CMM|C Chain C, Crystal Structure Of The Uba1-Ubiquitin Complex
Length = 1015
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 20/111 (18%)
Query: 24 QALLELEMNSDLKAQLRELYITRAKEIDLGGKKSVIVYVPMPQLKQFQKIQPRLVPKEID 83
+A+L+++ ++ L L+ L + AK + L G KS+ V+ P P Q + + E D
Sbjct: 20 EAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFDPEPV--QLADLSTQFFLTEKD 77
Query: 84 LGGKKSVI---------VYVP---------MPQLKQFQKIQPRLVRELEKK 116
+G K+ + YVP + QL QFQ + LE K
Sbjct: 78 IGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVVATDTVSLEDK 128
>pdb|4II2|A Chain A, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1)
In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg
pdb|4II3|A Chain A, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
pdb|4II3|C Chain C, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
Length = 1001
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/94 (22%), Positives = 46/94 (48%), Gaps = 4/94 (4%)
Query: 24 QALLELEMNSDLKAQLRELYITRAKEIDLGGKKSVIVYVPMPQLKQFQKIQPRLVPKEID 83
+A+ ++ ++ L + L + AK + L G KSV +Y P P + + + + E D
Sbjct: 19 EAMKQMSQSNVLIIGCKGLGVEIAKNVCLAGVKSVTLYDPQPT--RIEDLSSQYFLTEDD 76
Query: 84 LGGKKSVIVYVPMPQLKQFQKIQPRLVRELEKKF 117
+G ++ + + +L Q+ + +V EL ++
Sbjct: 77 IGVPRAKVTVSKLAELNQYVPVS--VVDELSTEY 108
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
0.319 0.139 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,835,831
Number of Sequences: 62578
Number of extensions: 215019
Number of successful extensions: 562
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 550
Number of HSP's gapped (non-prelim): 11
length of query: 224
length of database: 14,973,337
effective HSP length: 95
effective length of query: 129
effective length of database: 9,028,427
effective search space: 1164667083
effective search space used: 1164667083
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)