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= psy18093
(411 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GX8|A Chain A, The Crystal Stucture Of Bacillus Cereus Protein Related To
Nif3
pdb|2GX8|B Chain B, The Crystal Stucture Of Bacillus Cereus Protein Related To
Nif3
pdb|2GX8|C Chain C, The Crystal Stucture Of Bacillus Cereus Protein Related To
Nif3
Length = 397
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%)
Query: 88 DKWKERVVSTCLAHNIAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEKFNSMI 147
DK +++ C+ ++IA+Y+ HT D +GG+ND LA + L P+ E+ ++
Sbjct: 106 DKAYGKIIEKCIKNDIAIYAAHTNVDVAKGGVNDLLAEALGLQNTEVLAPTYAEEMKKVV 165
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 180 FAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEKFNSMI 224
A+Y+ HT D +GG+ND LA + L P+ E+ ++
Sbjct: 121 IAIYAAHTNVDVAKGGVNDLLAEALGLQNTEVLAPTYAEEMKKVV 165
>pdb|2FYW|A Chain A, Crystal Structure Of A Conserved Protein Of Unknown
Function From Streptococcus Pneumoniae
pdb|2FYW|B Chain B, Crystal Structure Of A Conserved Protein Of Unknown
Function From Streptococcus Pneumoniae
pdb|2FYW|C Chain C, Crystal Structure Of A Conserved Protein Of Unknown
Function From Streptococcus Pneumoniae
Length = 267
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 99 LAHNIAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEK 142
+ H+IAVY HT D ++ G+NDW I E L + PE+
Sbjct: 91 IKHDIAVYVSHTNIDIVENGLNDWFCQXLGIEETTYLQETGPER 134
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 34/134 (25%), Positives = 48/134 (35%), Gaps = 27/134 (20%)
Query: 180 FAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEKFNSMIAISHKINETDVVQHL 239
AVY HT D ++ G+NDW I E L + PE+ I
Sbjct: 95 IAVYVSHTNIDIVENGLNDWFCQXLGIEETTYLQETGPERGIGRIG-------------- 140
Query: 240 THIAEVAFGPQQAKESVTLFNPRYEIKASLISHDIPGHLSKENEIMINSIAVCAGSGGEL 299
PQ E +++ + H L K I+ +A+C GSG
Sbjct: 141 ------NIQPQTFWELAQQVKQVFDLDSLRXVHYQEDDLQKP----ISRVAICGGSGQSF 190
Query: 300 LR---GKKADLYIT 310
+ K AD+YIT
Sbjct: 191 YKDALAKGADVYIT 204
>pdb|2NYD|A Chain A, Crystal Structure Of Staphylococcus Aureus Hypothetical
Protein Sa1388
pdb|2NYD|B Chain B, Crystal Structure Of Staphylococcus Aureus Hypothetical
Protein Sa1388
Length = 370
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 345 FVTGEMSHHDVLDATHRGTTVLLLEHSDSERPFLQTMHTLLQIRLWHYLDWLKIYV--SK 402
FVTG++ HHD LDA G ++ + H SE + + TLL W ++ + I V S
Sbjct: 305 FVTGDIKHHDALDAKIHGVNLIDINHY-SEYVMKEGLKTLLM--NWFNIEKINIDVEAST 361
Query: 403 ADKDPIGYV 411
+ DP Y+
Sbjct: 362 INTDPFQYI 370
>pdb|3LNL|A Chain A, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
pdb|3LNL|B Chain B, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
Length = 370
Score = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 345 FVTGEMSHHDVLDATHRGTTVLLLEHSDSERPFLQTMHTLLQIRLWHYLDWLKIYV--SK 402
FVTG++ HHD LDA G ++ + H SE + + TLL W ++ + I V S
Sbjct: 305 FVTGDIKHHDALDAKIHGVNLIDINHY-SEYVMKEGLKTLLM--NWFNIEKINIDVEAST 361
Query: 403 ADKDPIGYV 411
+ DP Y+
Sbjct: 362 INTDPFQYI 370
>pdb|3O58|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|B Chain B, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 387
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 55/137 (40%), Gaps = 21/137 (15%)
Query: 180 FAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEKFNSMIAISHKINETDVVQHL 239
F YS D GI LA I +Y +V + + +I +T + Q
Sbjct: 130 FTKYSAKYAQDG--AGIERELA---RIKKYASVV---------RVLVHTQIRKTPLAQKK 175
Query: 240 THIAEVAFGPQQAKESVTLFNPRYEIKASLISHDIPGHLSKENEIMINSIAVCAGSGGEL 299
H+AE+ E V +E ++ S + ++NE MI++IAV G G E
Sbjct: 176 AHLAEIQLNGGSISEKVDWAREHFEKTVAVDS------VFEQNE-MIDAIAVTKGHGFEG 228
Query: 300 LRGKKADLYITDATHRG 316
+ + + THRG
Sbjct: 229 VTHRWGTKKLPRKTHRG 245
>pdb|3JYW|C Chain C, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 362
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 55/137 (40%), Gaps = 21/137 (15%)
Query: 180 FAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEKFNSMIAISHKINETDVVQHL 239
F YS D GI LA I +Y +V + + +I +T + Q
Sbjct: 126 FTKYSAKYAQDG--AGIERELA---RIKKYASVV---------RVLVHTQIRKTPLAQKK 171
Query: 240 THIAEVAFGPQQAKESVTLFNPRYEIKASLISHDIPGHLSKENEIMINSIAVCAGSGGEL 299
H+AE+ E V +E ++ S + ++NE MI++IAV G G E
Sbjct: 172 AHLAEIQLNGGSISEKVDWAREHFEKTVAVDS------VFEQNE-MIDAIAVTKGHGFEG 224
Query: 300 LRGKKADLYITDATHRG 316
+ + + THRG
Sbjct: 225 VTHRWGTKKLPRKTHRG 241
>pdb|1S1I|C Chain C, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 386
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 55/137 (40%), Gaps = 21/137 (15%)
Query: 180 FAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEKFNSMIAISHKINETDVVQHL 239
F YS D GI LA I +Y +V + + +I +T + Q
Sbjct: 129 FTKYSAKYAQDG--AGIERELA---RIKKYASVV---------RVLVHTQIRKTPLAQKK 174
Query: 240 THIAEVAFGPQQAKESVTLFNPRYEIKASLISHDIPGHLSKENEIMINSIAVCAGSGGEL 299
H+AE+ E V +E ++ S + ++NE MI++IAV G G E
Sbjct: 175 AHLAEIQLNGGSISEKVDWAREHFEKTVAVDS------VFEQNE-MIDAIAVTKGHGFEG 227
Query: 300 LRGKKADLYITDATHRG 316
+ + + THRG
Sbjct: 228 VTHRWGTKKLPRKTHRG 244
>pdb|3IZS|C Chain C, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
Length = 388
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 55/137 (40%), Gaps = 21/137 (15%)
Query: 180 FAVYSPHTTWDAIQGGINDWLASIYNISEYYPLVPSKPEKFNSMIAISHKINETDVVQHL 239
F YS D GI LA I +Y +V + + +I +T + Q
Sbjct: 130 FTKYSAKYAQDG--AGIERELA---RIKKYASVV---------RVLVHTQIRKTPLAQKK 175
Query: 240 THIAEVAFGPQQAKESVTLFNPRYEIKASLISHDIPGHLSKENEIMINSIAVCAGSGGEL 299
H+AE+ E V +E ++ S + ++NE MI++IAV G G E
Sbjct: 176 AHLAEIQLNGGSISEKVDWAREHFEKTVAVDS------VFEQNE-MIDAIAVTKGHGFEG 228
Query: 300 LRGKKADLYITDATHRG 316
+ + + THRG
Sbjct: 229 VTHRWGTKKLPRKTHRG 245
>pdb|1VKZ|A Chain A, Crystal Structure Of Phosphoribosylamine--Glycine Ligase
(Tm1250) From Thermotoga Maritima At 2.30 A Resolution
pdb|1VKZ|B Chain B, Crystal Structure Of Phosphoribosylamine--Glycine Ligase
(Tm1250) From Thermotoga Maritima At 2.30 A Resolution
Length = 412
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 33/123 (26%), Positives = 55/123 (44%), Gaps = 23/123 (18%)
Query: 195 GINDWLASIYN-ISEYYPLVPSK--PEKFNSMIAISHKINETDVVQHLTHIAEVAFGPQQ 251
G+++W ++++ + E L SK ++F I T EVA P++
Sbjct: 85 GVSNWRSNVFGPVKEVARLEGSKVYAKRFXKKYGIR------------TARFEVAETPEE 132
Query: 252 AKESVTLFNPRYEIKASLISHDIPGHL---SKENEIMINSIAVCAGSGGELLRGKKADLY 308
+E + F+P Y IKA ++ G L SKE I S + GEL++G K +
Sbjct: 133 LREKIKKFSPPYVIKADGLARG-KGVLILDSKEETIEKGSKLII----GELIKGVKGPVV 187
Query: 309 ITD 311
I +
Sbjct: 188 IDE 190
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
0.320 0.134 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,019,292
Number of Sequences: 62578
Number of extensions: 452535
Number of successful extensions: 1350
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1339
Number of HSP's gapped (non-prelim): 17
length of query: 411
length of database: 14,973,337
effective HSP length: 101
effective length of query: 310
effective length of database: 8,652,959
effective search space: 2682417290
effective search space used: 2682417290
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)