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= 005085
(715 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 = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 49/185 (26%), Positives = 70/185 (37%), Gaps = 15/185 (8%)
Query: 364 NCTGLAHIPSYVQNFNKLGNMIMAGCESLRCFPQNIHFISSIK-IDCYKCVNLKEFPR-- 420
+ GL +P Q F L + +A LR P +I ++ ++ + C L E P
Sbjct: 112 DAAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLNRLRELSIRACPELTELPEPL 170
Query: 421 ----ISG------NVVELNLMCTPIEEVPLSIECLPNLEILEMSFCYSLKRLSTSICXXX 470
SG N+ L L T I +P SI L NL+ L++ L L +I
Sbjct: 171 ASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNS-PLSALGPAIHHLP 229
Query: 471 XXXXXXXXXCINLESFPXXXXXXXXXXXXXXXXASNIKELPSSIENLEGLKQLKLTGCTK 530
C L ++P SN+ LP I L L++L L GC
Sbjct: 230 KLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVN 289
Query: 531 LGSLP 535
L LP
Sbjct: 290 LSRLP 294
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 46/105 (43%), Gaps = 8/105 (7%)
Query: 325 WEGQKKAPK-------LKYVDLNHSTNLTRIPEPSETPNLERMNLRNCTGLAHIPSYVQN 377
W G + P LK + + +S P P LE ++LR CT L + P
Sbjct: 192 WTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGG 251
Query: 378 FNKLGNMIMAGCESLRCFPQNIHFISSI-KIDCYKCVNLKEFPRI 421
L +I+ C +L P +IH ++ + K+D CVNL P +
Sbjct: 252 RAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSL 296
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 37/158 (23%), Positives = 70/158 (44%), Gaps = 21/158 (13%)
Query: 226 VCQEFREKPEKRSRLWDYKDVCHVLEKNKGTDAIKSIFLDLSKIEEINLDPRAFTNMSNV 285
C E E PE + +++G ++S+ L+ + I + P + N+ N+
Sbjct: 159 ACPELTELPEPLA-------STDASGEHQGLVNLQSLRLEWTGIRSL---PASIANLQNL 208
Query: 286 RLLKFYISGHFDVSKMSSKVH----LQQESYRTQLSFKKVEQIWEGQKKAPKLKYVDLNH 341
+ LK S +S + +H L++ R + + I+ G +AP LK + L
Sbjct: 209 KSLKIRNS---PLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGG--RAP-LKRLILKD 262
Query: 342 STNLTRIP-EPSETPNLERMNLRNCTGLAHIPSYVQNF 378
+NL +P + LE+++LR C L+ +PS +
Sbjct: 263 CSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQL 300
Score = 29.6 bits (65), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 507 IKELPSSIENLEGLKQLKLTGCTKLGSLPE 536
++ LP+SI +L L++L + C +L LPE
Sbjct: 139 LRALPASIASLNRLRELSIRACPELTELPE 168
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 55/218 (25%), Positives = 89/218 (40%), Gaps = 54/218 (24%)
Query: 1 MGGIGKTTIGVVFNQFSQKFEGKYFMANVREES----EKCGVLVHLRNQVLSKVLGENFD 56
M G GK+ + + EG F V S +K G+L+ L+N + E+F
Sbjct: 155 MAGCGKSVLAAEAVRDHSLLEG-CFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESF- 212
Query: 57 IGTQKIPQYIRDRLQRMKVF---------IVLDDV------------------NKDKTIL 89
+Q++P I + R++V ++LDDV +DK++
Sbjct: 213 --SQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVT 270
Query: 90 ER-YGTQRIYEVE-GLNCN---EVLRLFSSCAFKENHCPEDLLKHSETAVHYAKGNPLAL 144
+ G + + VE GL E+L LF N EDL + + + KG+PL +
Sbjct: 271 DSVMGPKHVVPVESGLGREKGLEILSLFV------NMKKEDLPAEAHSIIKECKGSPLVV 324
Query: 145 QVLGSSFYGKSKPD-WVNALNNL-----KRISGSDIYD 176
++G+ + P+ W L L KRI S YD
Sbjct: 325 SLIGALL--RDFPNRWAYYLRQLQNKQFKRIRKSSSYD 360
>pdb|1FNN|A Chain A, Crystal Structure Of Cdc6p From Pyrobaculum Aerophilum
pdb|1FNN|B Chain B, Crystal Structure Of Cdc6p From Pyrobaculum Aerophilum
Length = 389
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 33/142 (23%), Positives = 63/142 (44%), Gaps = 20/142 (14%)
Query: 113 SSCAFKENHCPEDLLK------HSETAVHYAKGNP-LALQVLGSSFYGKSKPDWVNALNN 165
+ E ED+L+ ++T + +G+ LA+ +L S Y + N
Sbjct: 206 AKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQ-------NG 258
Query: 166 LKRISGSDIYDDREHVMWILSDDYC---SVQYAMNVLVNKSLIKISYNK-LQMHDLLQEM 221
K I+ D+ + V++ +S++ + + +L +KIS+ + D E
Sbjct: 259 RKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGD--AEE 316
Query: 222 GREIVCQEFREKPEKRSRLWDY 243
+IVC+E+ E+P S+LW Y
Sbjct: 317 SYKIVCEEYGERPRVHSQLWSY 338
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 55/218 (25%), Positives = 88/218 (40%), Gaps = 54/218 (24%)
Query: 1 MGGIGKTTIGVVFNQFSQKFEGKYFMANVREES----EKCGVLVHLRNQVLSKVLGENFD 56
M G GK+ + + EG F V S +K G+L+ L+N + E+F
Sbjct: 162 MAGCGKSVLAAEAVRDHSLLEG-CFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESF- 219
Query: 57 IGTQKIPQYIRDRLQRMKVF---------IVLDDV------------------NKDKTIL 89
+Q++P I + R++V ++LDDV DK++
Sbjct: 220 --SQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTSDKSVT 277
Query: 90 ER-YGTQRIYEVE-GLNCN---EVLRLFSSCAFKENHCPEDLLKHSETAVHYAKGNPLAL 144
+ G + + VE GL E+L LF N EDL + + + KG+PL +
Sbjct: 278 DSVMGPKHVVPVESGLGREKGLEILSLFV------NMKKEDLPAEAHSIIKECKGSPLVV 331
Query: 145 QVLGSSFYGKSKPD-WVNALNNL-----KRISGSDIYD 176
++G+ + P+ W L L KRI S YD
Sbjct: 332 SLIGALL--RDFPNRWAYYLRQLQNKQFKRIRKSSSYD 367
>pdb|4GLP|A Chain A, The Crystal Structure Of Soluble Human Cd14 Reveals A Bent
Solenoid With A Hydrophobic Amino-terminal Pocket
Length = 310
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 316 LSFKKVEQIWEGQKKAPKLKYVDLNHSTNLTRIPEPSETPNLERMNL 362
LSF +EQ+ +G KL+ +DL+ S L R P+P E P ++ + L
Sbjct: 258 LSFAGLEQVPKGLPA--KLRVLDLS-SNRLNRAPQPDELPEVDNLTL 301
>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 = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 9/89 (10%)
Query: 351 PSETPNLERMNLRNCTGLAHIPSYVQNFNKLGNMIMAGCESLRCFPQNIHFISSIKIDCY 410
P+ P LER+ + + LA +P QN +L LR FP + ++++ +
Sbjct: 333 PALPPRLERL-IASFNHLAEVPELPQNLKQLH----VEYNPLREFPDIPESVEDLRMNSH 387
Query: 411 KCVNLKEFPRISGNVVELNLMCTPIEEVP 439
L E P + N+ +L++ P+ E P
Sbjct: 388 ----LAEVPELPQNLKQLHVETNPLREFP 412
>pdb|1V29|B Chain B, Crystal Structure Of Nitrile Hydratase From A Thermophile
Bacillus Smithii
Length = 229
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 10/104 (9%)
Query: 192 VQYAMNVLVNKSLIKISYNKLQMHDLLQEMGREIVCQEFREKPEKRSRLWDYKDVCHVLE 251
V Y + + ++YN L+ +L E E Q F EKP+ + + W+ + V+E
Sbjct: 65 VDYLTSSYYGHWIATVAYNLLET-GVLDEKELEDRTQAFMEKPDTKIQRWENPKLVKVVE 123
Query: 252 KNKGTDAIKSIFLDLSKIEEINLDPRAFTNMSNVRLLKFYISGH 295
K++ LS + E++ PR F ++ + +GH
Sbjct: 124 --------KALLEGLSPVREVSSFPR-FEVGERIKTRNIHPTGH 158
>pdb|4H08|A Chain A, Crystal Structure Of A Putative Hydrolase (Bt3161) From
Bacteroides Thetaiotaomicron Vpi-5482 At 1.80 A
Resolution
Length = 200
Score = 30.0 bits (66), Expect = 4.7, Method: Composition-based stats.
Identities = 28/94 (29%), Positives = 42/94 (44%), Gaps = 7/94 (7%)
Query: 296 FDVSKMSSKVH---LQQESYRTQLSFKKVEQIWEGQKKAPKLKYVDLNHSTNLTRIPEPS 352
FDV ++ +H +E Y SF K+ +I +K APK K + N + T
Sbjct: 75 FDVIHFNNGLHGFDYTEEEYDK--SFPKLIKII--RKYAPKAKLIWANTTPVRTGEGXKE 130
Query: 353 ETPNLERMNLRNCTGLAHIPSYVQNFNKLGNMIM 386
P ER+N+RN L HI N L +++
Sbjct: 131 FAPITERLNVRNQIALKHINRASIEVNDLWKVVI 164
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 0.137 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,234,520
Number of Sequences: 62578
Number of extensions: 821904
Number of successful extensions: 1711
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1700
Number of HSP's gapped (non-prelim): 18
length of query: 715
length of database: 14,973,337
effective HSP length: 106
effective length of query: 609
effective length of database: 8,340,069
effective search space: 5079102021
effective search space used: 5079102021
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)