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= 024879
(261 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U5C|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 255
Score = 265 bits (678), Expect = 1e-71, Method: Compositional matrix adjust.
Identities = 129/223 (57%), Positives = 163/223 (73%), Gaps = 1/223 (0%)
Query: 28 DWYDIKAPSCFRVRNVGKTLVTRTQGTKIASEGLKHRVFEVSLGDLHNEEEHAYRKIRLR 87
+W+DIKAPS F RNVGKTLV ++ G K AS+ LK RV EV L DL E+H++RKI+LR
Sbjct: 28 EWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVCLADLQGSEDHSFRKIKLR 87
Query: 88 AEDVQGKNVLTNFWGMDFTTDKLRSLVRKWHTLIEAYVDVKTTDNYTLRMFCIGFTKRLP 147
++VQGKN+LTNF GMDFTTDKLRS+VRKW TLIEA V VKT+D+Y LR+F I FT++
Sbjct: 88 VDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFAIAFTRKQA 147
Query: 148 NQVKRTCYAQASQIRQIRRKMREIMIAQAASCDLKGLVEKFIAEIIGREIEKATLSIYPL 207
NQVKR YAQ+S IR IR+ + EI+ + L L K I E+I +EIE AT I+PL
Sbjct: 148 NQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPL 207
Query: 208 QNVFIRKVKILKAPKFDLGKLMEVHGDYS-EDVGVKMERPADE 249
QN+ +RKVK+LK PKFD+G LM +HG+ S E+ G K+ DE
Sbjct: 208 QNIHVRKVKLLKQPKFDVGALMALHGEGSGEEKGKKVTGFKDE 250
>pdb|2XZM|4 Chain 4, 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|4 Chain 4, 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 = 265
Score = 194 bits (492), Expect = 5e-50, Method: Compositional matrix adjust.
Identities = 95/210 (45%), Positives = 138/210 (65%), Gaps = 4/210 (1%)
Query: 28 DWYDIKAPSCFRVRNVGKTLVTRTQGTKIASEGLKHRVFEVSLGDLH-NEEEHAYRKIRL 86
+WYD +AP F ++ GKTLVT++ G +IASE +K RV E +L DL N + A+RK++L
Sbjct: 30 EWYDFRAPIPFSSKSFGKTLVTKSSGNRIASEEIKGRVVESTLADLKDNSNDKAWRKVKL 89
Query: 87 RAEDVQGKNVLTNFWGMDFTTDKLRSLVRKWHTLIEAYVDVKTTDNYTLRMFCIGFTKRL 146
++V G+N T+F+G+D T D+L S++RKW TLIEA VD KT D Y +R+F + FTK+
Sbjct: 90 VIDEVDGRNAKTSFYGLDITRDRLCSMIRKWQTLIEARVDCKTNDGYIIRVFTLAFTKKT 149
Query: 147 P---NQVKRTCYAQASQIRQIRRKMREIMIAQAASCDLKGLVEKFIAEIIGREIEKATLS 203
TCYA++SQ+R IRRK+ + +AA + + I E ++IEK T +
Sbjct: 150 SAGKQSSTSTCYAKSSQVRAIRRKINTFITNEAAKLGIAEFSKNLIGEDYTKKIEKETKN 209
Query: 204 IYPLQNVFIRKVKILKAPKFDLGKLMEVHG 233
I+PLQN+ IRKVK+LK PK D K+ E++
Sbjct: 210 IFPLQNITIRKVKVLKRPKLDATKIAELYS 239
>pdb|3ZEY|0 Chain 0, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 256
Score = 180 bits (457), Expect = 6e-46, Method: Compositional matrix adjust.
Identities = 88/209 (42%), Positives = 132/209 (63%), Gaps = 2/209 (0%)
Query: 28 DWYDIKAPSCFRVRNVGKTLVTRTQGTKIASEGLKHRVFEVSLGDLH--NEEEHAYRKIR 85
+WYD+ AP F VR KT+ +TQGTKIA++ L+ RV+E +L DL+ E+ AYRK++
Sbjct: 28 EWYDVVAPKNFEVRQFAKTICNKTQGTKIAADFLRGRVYEGNLADLNKTQNEDDAYRKVK 87
Query: 86 LRAEDVQGKNVLTNFWGMDFTTDKLRSLVRKWHTLIEAYVDVKTTDNYTLRMFCIGFTKR 145
++VQG+N+LT F GMD T+D++ L+RKW T IEA V+ KT D Y LR+F I FTK+
Sbjct: 88 FTVQEVQGRNLLTQFHGMDMTSDRVYYLLRKWCTTIEATVEAKTADGYGLRLFLIAFTKK 147
Query: 146 LPNQVKRTCYAQASQIRQIRRKMREIMIAQAASCDLKGLVEKFIAEIIGREIEKATLSIY 205
NQ+ + CYA+ ++ +R + I+ + A D+ V I+ + K I
Sbjct: 148 QENQLSKNCYAKTRLVKWVRMRATNIIRRRLAKLDINDAVSLLTRNILRDRLAKRCNPII 207
Query: 206 PLQNVFIRKVKILKAPKFDLGKLMEVHGD 234
PL+++ IRKVK+++ PKFD L+ HG+
Sbjct: 208 PLRDLRIRKVKVIRTPKFDAQALIAAHGE 236
>pdb|3J20|A Chain A, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 198
Score = 94.0 bits (232), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 64/194 (32%), Positives = 94/194 (48%), Gaps = 16/194 (8%)
Query: 29 WYDIKAPSCFRVRNVGKTLVTRTQGTKIASEGLKHRVFEVSLGDLHNEEEHAYRKIRLRA 88
WY I AP F VG T E + +RV EV+L D+ + ++ K+ +
Sbjct: 18 WYIIYAPDFFGGVEVGLTPAD-------DPEKVLNRVVEVTLKDVTGDFTKSHVKLYFQV 70
Query: 89 EDVQGKNVLTNFWGMDFTTDKLRSLVRKWHTLIEAYVDVKTTDNYTLRMFCIGFTKRLPN 148
DV+G+N T F GM +RSLVR+ T I+ ++ T D Y LR+ + R
Sbjct: 71 YDVKGQNAYTKFKGMKLARSYIRSLVRRKTTRIDGIFNITTKDGYKLRVMAMAIAMRR-- 128
Query: 149 QVKRTCYAQASQIRQIRRKMREIMIAQAASCDLKGLVEKFIAEIIGREIEKATLSIYPLQ 208
Q SQ R IR+ M+EI+ +A + K V + + I EI K IYPL+
Sbjct: 129 -------IQTSQERAIRKIMQEIIYKKAEELNFKDFVLESVNGKIAAEIAKEAKKIYPLR 181
Query: 209 NVFIRKVKILKAPK 222
IRK+K+L+ P+
Sbjct: 182 KAEIRKIKVLEEPQ 195
>pdb|2G36|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase (Ec
6.1.1.2) (Tryptophan-Trna Ligase)(Trprs) (Tm0492) From
Thermotoga Maritima At 2.50 A Resolution
Length = 340
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 30/141 (21%), Positives = 52/141 (36%), Gaps = 3/141 (2%)
Query: 113 LVRKWHTLIEAYVDVKTTDNYTLRMFCIGFTKRLPNQVKRTCYAQASQIRQIRRKMREIM 172
V WH L Y DV YT R GF + K + Q+ + M
Sbjct: 50 FVADWHALTTHYDDVSKLKEYT-RDLVRGFLACGIDPEKSVIFVQSGVKEHAELALLFSM 108
Query: 173 IAQAASCDLKGLVEKFIAEIIGREIEKATLSIYPLQNVFIRKVKILKAPKFDLGKLMEVH 232
I + + ++ +E+ +++ A IYP+ + I KA +G+ H
Sbjct: 109 IVSVSRLERVPTYKEIKSELNYKDLSTAGFLIYPVLQA--ADILIYKAEGVPVGEDQVYH 166
Query: 233 GDYSEDVGVKMERPADEPIPE 253
+ + ++ + DE PE
Sbjct: 167 IELTREIARRFNYLYDEVFPE 187
>pdb|2R76|A Chain A, Crystal Structure Of The Rare Lipoprotein B (So_1173) From
Shewanella Oneidensis, Northeast Structural Genomics
Consortium Target Sor91a
pdb|2R76|B Chain B, Crystal Structure Of The Rare Lipoprotein B (So_1173) From
Shewanella Oneidensis, Northeast Structural Genomics
Consortium Target Sor91a
Length = 152
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 138 FCIGFTKRLPNQVKRTCYAQASQIRQIRRKMRE-IMIAQAASCDLKGLVEKFIAEIIGRE 196
F + + ++P Q+ + + + + +++ R +RE + + D V + +I
Sbjct: 3 FKLQRSYQIPEQLNQLSLSSSDEYKELTRLVRERLRLNNVKIVDAANDVP--VLRLITDS 60
Query: 197 IEKATLSIYPLQNV 210
+E++TLS+YP NV
Sbjct: 61 LERSTLSLYPTGNV 74
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 0.137 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,556,851
Number of Sequences: 62578
Number of extensions: 251349
Number of successful extensions: 579
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 568
Number of HSP's gapped (non-prelim): 11
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
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: 50 (23.9 bits)