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= 004707
(734 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 40/89 (44%), Gaps = 1/89 (1%)
Query: 251 LKSLVDLFLHGCLNLERFPEILEKMEHLKHIYLQR-TAITELPSSFENLLGLESLSVRGC 309
L L +L L GC L +P I LK + L+ + + LP L LE L +RGC
Sbjct: 228 LPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGC 287
Query: 310 SKLDKLPDNIGNLESLAYILADGSAISQL 338
L +LP I L + IL +QL
Sbjct: 288 VNLSRLPSLIAQLPANCIILVPPHLQAQL 316
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/148 (23%), Positives = 62/148 (41%), Gaps = 34/148 (22%)
Query: 265 LERFPEILEKMEHLKHIYLQRTAITELPSSFENLLGLESLSVRGCSKLDKLPDNIGNLES 324
L P+ ++ L+ + L R + LP+S +L L LS+R C +L +LP+ + + ++
Sbjct: 116 LXELPDTXQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDA 175
Query: 325 ---------LAYILADGSAISQLPSSVADSNVLRYLWFPRCRNXXXXXXXXXXXXXXXXX 375
L + + + I LP+S+A+ L+ L
Sbjct: 176 SGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSL------------------------ 211
Query: 376 XXXRDCAVTDIPQEIGCLSSLEELDLSG 403
R+ ++ + I L LEELDL G
Sbjct: 212 -KIRNSPLSALGPAIHHLPKLEELDLRG 238
>pdb|1G9U|A Chain A, Crystal Structure Of Yopm-leucine Rich Effector Protein
From Yersinia Pestis
pdb|1JL5|A Chain A, Novel Molecular Architecture Of Yopm-A Leucine-Rich
Effector Protein From Yersinia Pestis
Length = 454
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 55/209 (26%), Positives = 82/209 (39%), Gaps = 47/209 (22%)
Query: 247 RFCKLKSLVDLFLHGCLNLERFPEILEKMEHLKHIYLQRTAITELPSSFENLLGLESLSV 306
+ L ++ G LE PE L+ + L IY ++ +LP L LES+ V
Sbjct: 167 KLPDLPPSLEFIAAGNNQLEELPE-LQNLPFLTAIYADNNSLKKLPDLP---LSLESI-V 221
Query: 307 RGCSKLDKLPDNIGNLESLAYILADGS---AISQLPSSVADSNVLRYLWFPRCRNXXXXX 363
G + L++LP+ + NL L I AD + + LP S+ NV
Sbjct: 222 AGNNILEELPE-LQNLPFLTTIYADNNLLKTLPDLPPSLEALNV---------------- 264
Query: 364 XXXXXXXXXXXXXXXRDCAVTDIPQEIGCLSSLEELDLSGNSFESLPVSIKXXXXXXXXX 423
RD +TD+P+ SL LD+S N F L
Sbjct: 265 ---------------RDNYLTDLPE---LPQSLTFLDVSENIFSGL----SELPPNLYYL 302
Query: 424 XXXCNMLRSLPELPSCLGFLNLSGCNMLQ 452
N +RSL +LP L LN+S +++
Sbjct: 303 NASSNEIRSLCDLPPSLEELNVSNNKLIE 331
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 274 KMEHLKHIYLQRTAITELPSSFENLLGLESLSVRGCSKLDKLPDNIGNLESLAYILADGS 333
K + L +YL ++TELP+ +NL L L + ++L LP +G+ L Y +
Sbjct: 245 KYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDL-SHNRLTSLPAELGSCFQLKYFYFFDN 303
Query: 334 AISQLPSSVADSNVLRYL 351
++ LP + L++L
Sbjct: 304 MVTTLPWEFGNLCNLQFL 321
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 382 AVTDIPQEIGCLSSLEELDLSGNSFESLPVSI 413
++T++P EI LS+L LDLS N SLP +
Sbjct: 258 SLTELPAEIKNLSNLRVLDLSHNRLTSLPAEL 289
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 33.5 bits (75), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 54/238 (22%), Positives = 100/238 (42%), Gaps = 44/238 (18%)
Query: 2 KVLIVLDDVNKDEQLEGLIGGLDQYGPGSRIVVTTRDKGVLEN-FGVEKIYRVNGXXXXX 60
+ L++LDDV L+ + +I++TTRDK V ++ G + + V
Sbjct: 237 RSLLILDDVWDPWVLKA-------FDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGRE 289
Query: 61 XXXXXXXXXXKENHCPEDFKRDSRRVVKYADGNPLVLKVLGSSLKR-KSHWGNVLDDLN- 118
N ED ++ ++K G+PLV+ ++G+ L+ + W L L
Sbjct: 290 KGLEILSLFV--NMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQN 347
Query: 119 ----RICESDIHD---IHDILKISFNELMPKMKSIFLDIACFFEGEDKDFVTRIL----- 166
RI +S +D + + + IS L +K + D++ +D T++L
Sbjct: 348 KQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSIL--QKDVKVPTKVLCVLWD 405
Query: 167 --DDYGSYGLEVLIDKSLITVSHN----CLRMHDL------------LQEMGREIVRQ 206
+ L+ ++KSL+ + N C +HDL LQ++ R++V Q
Sbjct: 406 LETEEVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQ 463
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 72/162 (44%), Gaps = 34/162 (20%)
Query: 77 EDFKRDSRRVVKYADGNPLVLKVLGSSLKR-KSHWGNVLDDLN-----RICESDIHD--- 127
ED ++ ++K G+PLV+ ++G+ L+ + W L L RI +S +D
Sbjct: 311 EDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEA 370
Query: 128 IHDILKISFNELMPKMKSIFLDIACFFEGEDKDFVTRIL-------DDYGSYGLEVLIDK 180
+ + + IS L +K + D++ +D T++L + L+ ++K
Sbjct: 371 LDEAMSISVEMLREDIKDYYTDLSIL--QKDVKVPTKVLCVLWDLETEEVEDILQEFVNK 428
Query: 181 SLITVSHN----CLRMHDL------------LQEMGREIVRQ 206
SL+ + N C +HDL LQ++ R++V Q
Sbjct: 429 SLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQ 470
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 33/120 (27%), Positives = 56/120 (46%), Gaps = 11/120 (9%)
Query: 248 FCKLKSLVDLFLHGCLNLERFP-EILEKMEHLKHIYLQRTAITELPSS-FENLLGLESLS 305
F L +L +L+L G L P + + + L + L +T LPS+ F+ L+ L+ L
Sbjct: 60 FDSLINLKELYL-GSNQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKEL- 117
Query: 306 VRGCSKLDKLPDNIGNLESLAYILADGSAISQLP-------SSVADSNVLRYLWFPRCRN 358
C+KL +LP I L L ++ D + + +P SS+ + + W CR+
Sbjct: 118 FMCCNKLTELPRGIERLTHLTHLALDQNQLKSIPHGAFDRLSSLTHAYLFGNPWDCECRD 177
>pdb|3CVR|A Chain A, Crystal Structure Of The Full Length Ipah3
Length = 571
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 44/108 (40%), Gaps = 9/108 (8%)
Query: 382 AVTDIPQEIGCLSSLEELDLSGNSFESLPVSIKXXXXXXXXXXXXCNMLRSLPELPSCLG 441
A+ +P+ L L+ D ++ LP S+K N L LPELP+ L
Sbjct: 91 ALISLPELPASLEYLDACDNRLSTLPELPASLKHLDVDN-------NQLTXLPELPALLE 143
Query: 442 FLNLSGCNMLQSXXXXXXXXXXXXAGNCKLLQSLPEIRSSVEELDASV 489
++N + N L N + L LPE+ S+E LD S
Sbjct: 144 YIN-ADNNQLTXLPELPTSLEVLSVRNNQ-LTFLPELPESLEALDVST 189
>pdb|1S1H|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,
1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is
In File 1s1i
Length = 192
Score = 30.4 bits (67), Expect = 4.0, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 24/50 (48%)
Query: 154 FEGEDKDFVTRILDDYGSYGLEVLIDKSLITVSHNCLRMHDLLQEMGREI 203
F E +F TR L + G G+EV + + V R D+L E GR I
Sbjct: 16 FYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRI 65
>pdb|3JYV|C Chain C, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
Lanuginosus Ribosome At 8.9a Resolution
Length = 188
Score = 30.4 bits (67), Expect = 4.0, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 24/50 (48%)
Query: 154 FEGEDKDFVTRILDDYGSYGLEVLIDKSLITVSHNCLRMHDLLQEMGREI 203
F E +F TR L + G G+EV + + V R D+L E GR I
Sbjct: 12 FYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRI 61
>pdb|3IZB|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 240
Score = 30.4 bits (67), Expect = 4.0, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 24/50 (48%)
Query: 154 FEGEDKDFVTRILDDYGSYGLEVLIDKSLITVSHNCLRMHDLLQEMGREI 203
F E +F TR L + G G+EV + + V R D+L E GR I
Sbjct: 17 FYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRI 66
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 37/157 (23%), Positives = 65/157 (41%), Gaps = 17/157 (10%)
Query: 4 LIVLDDVNKDEQLEGLIGGLDQYGPGSRIVVTTRDKGVLENFGVEKIYRVNGXXXXXXXX 63
L++LDDV L+ + +I++TTRDK V ++ K Y V
Sbjct: 239 LLILDDVWDSWVLKA-------FDSQCQILLTTRDKSVTDSVMGPK-YVVPVESSLGKEK 290
Query: 64 XXXXXXXKENHCPEDFKRDSRRVVKYADGNPLVLKVLGSSLKR-KSHWGNVLDDLN---- 118
N D + ++K G+PLV+ ++G+ L+ + W L L
Sbjct: 291 GLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQF 350
Query: 119 -RICESDIHD---IHDILKISFNELMPKMKSIFLDIA 151
RI +S +D + + + IS L +K + D++
Sbjct: 351 KRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLS 387
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 37/159 (23%), Positives = 66/159 (41%), Gaps = 17/159 (10%)
Query: 2 KVLIVLDDVNKDEQLEGLIGGLDQYGPGSRIVVTTRDKGVLENFGVEKIYRVNGXXXXXX 61
+ L++LDDV L+ + +I++TTRDK V ++ K Y V
Sbjct: 243 RSLLILDDVWDSWVLKA-------FDSQCQILLTTRDKSVTDSVMGPK-YVVPVESSLGK 294
Query: 62 XXXXXXXXXKENHCPEDFKRDSRRVVKYADGNPLVLKVLGSSLKR-KSHWGNVLDDLN-- 118
N D + ++K G+PLV+ ++G+ L+ + W L L
Sbjct: 295 EKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNK 354
Query: 119 ---RICESDIHD---IHDILKISFNELMPKMKSIFLDIA 151
RI +S +D + + + IS L +K + D++
Sbjct: 355 QFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLS 393
>pdb|3OPY|I Chain I, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|J Chain J, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|K Chain K, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|L Chain L, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
Length = 351
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 133 KISFNELMPKMKSIFL---DIACFFEGEDKDFVTRILDDYGSYGLEVLIDKSLITVSHNC 189
KI+F+ L K + L D FE D+ FVT +LD Y G ID L+T + +
Sbjct: 192 KITFHLLCKKTARMILVGDDRETDFEMSDRSFVTLLLDYYQRVGTTKKIDLLLLTNNFDT 251
Query: 190 LRMHDLLQEM 199
M++ LQ++
Sbjct: 252 -NMNNKLQQL 260
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 0.139 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,506,164
Number of Sequences: 62578
Number of extensions: 744006
Number of successful extensions: 1831
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1794
Number of HSP's gapped (non-prelim): 49
length of query: 734
length of database: 14,973,337
effective HSP length: 106
effective length of query: 628
effective length of database: 8,340,069
effective search space: 5237563332
effective search space used: 5237563332
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: 55 (25.8 bits)