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= 039689
(763 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 68/163 (41%), Gaps = 30/163 (18%)
Query: 16 LNMHQS-LKEVGQKIAMKCKGLPLAAKTLGGLLRGKDDPKDWENVL------------KT 62
+NM ++ L E I +CKG PL +G LLR D P WE L K+
Sbjct: 305 VNMKKADLPEQAHSIIKECKGSPLVVSLIGALLR--DFPNRWEYYLKQLQNKQFKRIRKS 362
Query: 63 EVWDLADDKCDIIPALRVSYHFLPPQLKQCFAYCSLFPKDHEFQKEQIILLWAAEGFLHQ 122
+D + A+ +S L +K + S+ KD + + + +LW E
Sbjct: 363 SSYDYE----ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME----- 413
Query: 123 ENSKRKMEDLGREFVEELHSRSLFHQSTYDASRFVMHDLINDL 165
++ED+ +EFV + LF + R+ +HDL D
Sbjct: 414 ---TEEVEDILQEFVNK---SLLFCDRNGKSFRYYLHDLQVDF 450
>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 = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 75/177 (42%), Gaps = 33/177 (18%)
Query: 16 LNMHQS-LKEVGQKIAMKCKGLPLAAKTLGGLLRGKDDPKDWENVL------------KT 62
+NM ++ L E I +CKG PL +G LLR D P WE L K+
Sbjct: 299 VNMKKADLPEQAHSIIKECKGSPLVVSLIGALLR--DFPNRWEYYLKQLQNKQFKRIRKS 356
Query: 63 EVWDLADDKCDIIPALRVSYHFLPPQLKQCFAYCSLFPKDHEFQKEQIILLWAAEGFLHQ 122
+D + A+ +S L +K + S+ KD + + + +LW E
Sbjct: 357 SSYDYE----ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME----- 407
Query: 123 ENSKRKMEDLGREFVEELHSRSLFHQSTYDASRFVMHDLINDLTRWAAGETCFRMED 179
++ED+ +EFV + LF + R+ +HDL D + + C +++D
Sbjct: 408 ---TEEVEDILQEFV---NKSLLFCDRNGKSFRYYLHDLQVD---FLTEKNCSQLQD 455
>pdb|4H09|A Chain A, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Eubven_01088) From Eubacterium Ventriosum Atcc
27560 At 2.50 A Resolution
pdb|4H09|B Chain B, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Eubven_01088) From Eubacterium Ventriosum Atcc
27560 At 2.50 A Resolution
pdb|4H09|C Chain C, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Eubven_01088) From Eubacterium Ventriosum Atcc
27560 At 2.50 A Resolution
pdb|4H09|D Chain D, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Eubven_01088) From Eubacterium Ventriosum Atcc
27560 At 2.50 A Resolution
pdb|4H09|E Chain E, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Eubven_01088) From Eubacterium Ventriosum Atcc
27560 At 2.50 A Resolution
Length = 379
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 32/163 (19%), Positives = 68/163 (41%), Gaps = 19/163 (11%)
Query: 467 LQCLPALRELEIDGCKGVVLSSPTDLSSLKLVHSRDMAKEVFEQGLPKLERLEIQHVREQ 526
L+ PA + G + + S+ +++ + +++ K G+ L +
Sbjct: 187 LESYPAAKT----GTEFTIPSTVKTVTAYGFSYGKNLKKITITSGVTTLGDGAFYGXKA- 241
Query: 527 TYLWRSETRLPQDIRSLNRLQISRCPQLISL-----LRTVKIEDCNALESLPEAWMHNSN 581
E +P+++ S+ + C L +L ++TV C+ +L + NS
Sbjct: 242 ----LDEIAIPKNVTSIGSFLLQNCTALKTLNFYAKVKTVPYLLCSGCSNLTKVVXDNS- 296
Query: 582 SSLESLKIRSCNSLVSFPDFALPSQLRTVTI---KGCDALESL 621
++E+L+ R V LP+ L+T+ + K C AL ++
Sbjct: 297 -AIETLEPRVFXDCVKLSSVTLPTALKTIQVYAFKNCKALSTI 338
>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 = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 204 LRGYNIFELPKAIENLKHLRFLDLSTTKIEILRESINTLYNLHTLLLEDCRRLKKLCKDM 263
L G ++ ELP I+NL +LR LDLS ++ L + + + L D + L +
Sbjct: 254 LNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFD-NMVTTLPWEF 312
Query: 264 GNLTKLHHL 272
GNL L L
Sbjct: 313 GNLCNLQFL 321
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 33.5 bits (75), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 61/158 (38%), Gaps = 29/158 (18%)
Query: 20 QSLKEVGQKIAMKCKGLPLAAKTLGGLLRGKDDPKDWENVL------------KTEVWDL 67
+ L I +CKG PL +G LLR D P W L K+ +D
Sbjct: 311 EDLPAEAHSIIKECKGSPLVVSLIGALLR--DFPNRWAYYLRQLQNKQFKRIRKSSSYDY 368
Query: 68 ADDKCDIIPALRVSYHFLPPQLKQCFAYCSLFPKDHEFQKEQIILLWAAEGFLHQENSKR 127
+ A+ +S L +K + S+ KD + + + +LW E
Sbjct: 369 E----ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE--------TE 416
Query: 128 KMEDLGREFVEELHSRSLFHQSTYDASRFVMHDLINDL 165
++ED+ +EFV + LF + + +HDL D
Sbjct: 417 EVEDILQEFVNK---SLLFCNRNGKSFCYYLHDLQVDF 451
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 61/158 (38%), Gaps = 29/158 (18%)
Query: 20 QSLKEVGQKIAMKCKGLPLAAKTLGGLLRGKDDPKDWENVL------------KTEVWDL 67
+ L I +CKG PL +G LLR D P W L K+ +D
Sbjct: 304 EDLPAEAHSIIKECKGSPLVVSLIGALLR--DFPNRWAYYLRQLQNKQFKRIRKSSSYDY 361
Query: 68 ADDKCDIIPALRVSYHFLPPQLKQCFAYCSLFPKDHEFQKEQIILLWAAEGFLHQENSKR 127
+ A+ +S L +K + S+ KD + + + +LW E
Sbjct: 362 E----ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE--------TE 409
Query: 128 KMEDLGREFVEELHSRSLFHQSTYDASRFVMHDLINDL 165
++ED+ +EFV + LF + + +HDL D
Sbjct: 410 EVEDILQEFVNK---SLLFCNRNGKSFCYYLHDLQVDF 444
>pdb|1A5D|A Chain A, Gammae Crystallin From Rat Lens
pdb|1A5D|B Chain B, Gammae Crystallin From Rat Lens
pdb|1ZGT|A Chain A, Structure Of Hydrogenated Rat Gamma E Crystallin In H2o
pdb|1ZIE|A Chain A, Hydrogenated Gammae Crystallin In D2o Solvent
pdb|1ZIQ|A Chain A, Deuterated Gammae Crystallin In D2o Solvent
pdb|1ZIR|A Chain A, Deuterated Gammae Crystallin In H2o Solvent
Length = 173
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 18/93 (19%), Positives = 42/93 (45%), Gaps = 9/93 (9%)
Query: 663 RCDNLRFNSLRKLKISGGCPDLVSSPRFPASLTELKISDMPSLERLSSIGENLTSLKFLD 722
RC+++R +S GC L P F L+ D P ++ +++ S + +
Sbjct: 31 RCNSVRVDS--------GCWMLYEQPNFTGCQYFLRRGDYPDYQQWMGFSDSVRSCRLIP 82
Query: 723 LDNCPKLKYFSKQGLPKSLLRLIIDECPLIEKR 755
+ +++ + ++ ++ I D+CP ++ R
Sbjct: 83 HSSSHRIRIYEREDYRGQMVE-ITDDCPHLQDR 114
>pdb|2WFH|A Chain A, The Human Slit 2 Dimerization Domain D4
pdb|2WFH|B Chain B, The Human Slit 2 Dimerization Domain D4
Length = 193
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 204 LRGYNIFELPKAIENLKHLRFLDLSTTKIEIL-RESINTLYNLHTLLLE 251
L G +PK + N KHL +DLS +I L +S + + L TL+L
Sbjct: 38 LDGNQFTLVPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILS 86
>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 = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 47/143 (32%), Positives = 66/143 (46%), Gaps = 32/143 (22%)
Query: 568 ALESLPEAWMHNSNSSLESLKIRSCNSLVSFPDFALPSQLRTVTIKGCD--ALESLPEAW 625
L SLPE H LESL + SCNSL P+ LP L+++ + + AL LP
Sbjct: 82 GLSSLPELPPH-----LESL-VASCNSLTELPE--LPQSLKSLLVDNNNLKALSDLPPL- 132
Query: 626 MQNSSTSLESLAIDSCDSLTYIARIQLPPSLKRLIIFRCDNLRFNSLRKLKISGGCPDLV 685
LE L + S + L + +Q + L I DN NSL+KL PDL
Sbjct: 133 -------LEYLGV-SNNQLEKLPELQ---NSSFLKIIDVDN---NSLKKL------PDLP 172
Query: 686 SSPRFPASLTELKISDMPSLERL 708
S F A+ ++ ++P L+ L
Sbjct: 173 PSLEFIAAGNN-QLEELPELQNL 194
>pdb|3CVR|A Chain A, Crystal Structure Of The Full Length Ipah3
Length = 571
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 684 LVSSPRFPASLTELKISDMPSLERLSSIGENLTSLKFLDLDN 725
L+S P PASL L D RLS++ E SLK LD+DN
Sbjct: 92 LISLPELPASLEYLDACD----NRLSTLPELPASLKHLDVDN 129
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 7/51 (13%)
Query: 213 PKAIENLKHLRFLDLSTTKIEILRESI-NTLYNLHTLLLE------DCRRL 256
P A L +LR L++S ++ L ES+ +++ NL TL+L+ DCR L
Sbjct: 289 PYAFRGLNYLRVLNVSGNQLTTLEESVFHSVGNLETLILDSNPLACDCRLL 339
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 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,874,021
Number of Sequences: 62578
Number of extensions: 801178
Number of successful extensions: 1773
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1764
Number of HSP's gapped (non-prelim): 21
length of query: 763
length of database: 14,973,337
effective HSP length: 106
effective length of query: 657
effective length of database: 8,340,069
effective search space: 5479425333
effective search space used: 5479425333
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: 55 (25.8 bits)