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= 003996
(780 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 62/238 (26%), Positives = 101/238 (42%), Gaps = 38/238 (15%)
Query: 157 FESRVSTLKSIQNALTDAN--VSIIGVYGMGGIGKTTLVKEFVRQAS--ENKLFDRVVFS 212
F +R + +IQ L N + +YGM G GK+ L E VR S E V +
Sbjct: 126 FVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWV 185
Query: 213 EVSQTPD---IKKIQG---------EIAEKLGLELSDEAEYRRASRLYERLKNENKILVI 260
+ + + K+Q +++L L + + + R L+ + L+I
Sbjct: 186 SIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVL----MLRKHPRSLLI 241
Query: 261 LDNIWKHLDLDTVGIPFGNDHEGCRLLLTARDINVLLS-MGSKDNFLI-GNLNEE---EA 315
LD++W L F N C++LLT RD +V S MG K + L E E
Sbjct: 242 LDDVWDPWVLKA----FDNQ---CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEI 294
Query: 316 WRLFKIMNGDDVENCKFKSTAINVAQACGGLPIALTTVARALRNKSLHEWKNALRELQ 373
LF M +D+ + A ++ + C G P+ ++ + LR+ + W LR+LQ
Sbjct: 295 LSLFVNMKKEDL-----PAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQ 346
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 61/238 (25%), Positives = 100/238 (42%), Gaps = 38/238 (15%)
Query: 157 FESRVSTLKSIQNALTDAN--VSIIGVYGMGGIGKTTLVKEFVRQAS--ENKLFDRVVFS 212
F +R + +IQ L N + +YGM G GK+ L E VR S E V +
Sbjct: 133 FVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWV 192
Query: 213 EVSQTPD---IKKIQG---------EIAEKLGLELSDEAEYRRASRLYERLKNENKILVI 260
+ + + K+Q +++L L + + + R L+ + L+I
Sbjct: 193 SIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVL----MLRKHPRSLLI 248
Query: 261 LDNIWKHLDLDTVGIPFGNDHEGCRLLLTARDINVLLS-MGSKDNFLI-GNLNEE---EA 315
LD++W L F N C++LLT D +V S MG K + L E E
Sbjct: 249 LDDVWDPWVLKA----FDNQ---CQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEI 301
Query: 316 WRLFKIMNGDDVENCKFKSTAINVAQACGGLPIALTTVARALRNKSLHEWKNALRELQ 373
LF M +D+ + A ++ + C G P+ ++ + LR+ + W LR+LQ
Sbjct: 302 LSLFVNMKKEDL-----PAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQ 353
>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 = 54/255 (21%), Positives = 105/255 (41%), Gaps = 32/255 (12%)
Query: 156 AFESRVSTLKSIQNALTD--ANVSIIGVYGMGGIGKTTLVKEFVRQAS--ENKLFDRVVF 211
F +R + +IQ L+ + ++GM G GK+ L E VR S E V +
Sbjct: 125 VFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHW 184
Query: 212 SEVSQTPD---IKKIQG---------EIAEKLGLELSDEAEYRRASRLYERLKNENKILV 259
V + + K+Q +++L L + + + R L+ + L+
Sbjct: 185 VSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRIL----MLRKHPRSLL 240
Query: 260 ILDNIWKHLDLDTVGIPFGNDHEGCRLLLTARDINVLLS-MGSKDNFLI-GNLNEEEAWR 317
ILD++W L C++LLT RD +V S MG K + +L +E+
Sbjct: 241 ILDDVWDSWVLKAFD-------SQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLE 293
Query: 318 LFKIMNGDDVENCKFKSTAINVAQACGGLPIALTTVARALRNKSLHEWKNALRELQTPSV 377
+ + +++ A ++ + C G P+ ++ + LR+ + W+ L++LQ
Sbjct: 294 ILSLFV--NMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQNKQF 350
Query: 378 VNFEGVPAETYSSIE 392
+ Y +++
Sbjct: 351 KRIRKSSSYDYEALD 365
>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 = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 54/255 (21%), Positives = 105/255 (41%), Gaps = 32/255 (12%)
Query: 156 AFESRVSTLKSIQNALTD--ANVSIIGVYGMGGIGKTTLVKEFVRQAS--ENKLFDRVVF 211
F +R + +IQ L+ + ++GM G GK+ L E VR S E V +
Sbjct: 131 VFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHW 190
Query: 212 SEVSQTPD---IKKIQG---------EIAEKLGLELSDEAEYRRASRLYERLKNENKILV 259
V + + K+Q +++L L + + + R L+ + L+
Sbjct: 191 VSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRIL----MLRKHPRSLL 246
Query: 260 ILDNIWKHLDLDTVGIPFGNDHEGCRLLLTARDINVLLS-MGSKDNFLI-GNLNEEEAWR 317
ILD++W L C++LLT RD +V S MG K + +L +E+
Sbjct: 247 ILDDVWDSWVLKAFD-------SQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLE 299
Query: 318 LFKIMNGDDVENCKFKSTAINVAQACGGLPIALTTVARALRNKSLHEWKNALRELQTPSV 377
+ + +++ A ++ + C G P+ ++ + LR+ + W+ L++LQ
Sbjct: 300 ILSLFV--NMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQNKQF 356
Query: 378 VNFEGVPAETYSSIE 392
+ Y +++
Sbjct: 357 KRIRKSSSYDYEALD 371
>pdb|3GGR|B Chain B, Crystal Structure Of The Human Rad9-Hus1-Rad1 Complex
Length = 286
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 385 AETYSSIELSFKYLKGEQLKKIFQLCSLIGNSFCLIDLLRYSMGLGIF 432
AE + I ++L G+Q+ LC+++ N DLL + L F
Sbjct: 234 AEVHIDIRKLLQFLAGQQVNPTKALCNIVNNKMVHFDLLHEDVSLQYF 281
>pdb|1W5S|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
pdb|1W5S|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
pdb|1W5T|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
pdb|1W5T|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
pdb|1W5T|C Chain C, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
Length = 412
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 142 IPEEIWLKSNKGYEAFESRVSTLKSIQNA-LTDANVSIIGVYGMGGIGKTTLVKEFVRQA 200
IP E L+ +G +R+ + + A L+D N+ I G G GIGKTTL K V++
Sbjct: 20 IPPE--LRVRRGEAEALARIYLNRLLSGAGLSDVNM-IYGSIGRVGIGKTTLAKFTVKRV 76
Query: 201 SE 202
SE
Sbjct: 77 SE 78
>pdb|3G65|C Chain C, Crystal Structure Of The Human Rad9-Rad1-Hus1 Dna Damage
Checkpoint Complex
Length = 280
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 385 AETYSSIELSFKYLKGEQLKKIFQLCSLIGNSFCLIDLLRYSMGLGIF 432
AE + I ++L G+Q+ LC+++ N DLL + L F
Sbjct: 228 AEVHIDIRKLLQFLAGQQVNPTKALCNIVNNKMVHFDLLHEDVSLQYF 275
>pdb|3A1J|B Chain B, Crystal Structure Of The Human Rad9-Hus1-Rad1 Complex
Length = 281
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 385 AETYSSIELSFKYLKGEQLKKIFQLCSLIGNSFCLIDLLRYSMGLGIF 432
AE + I ++L G+Q+ LC+++ N DLL + L F
Sbjct: 229 AEVHIDIRKLLQFLAGQQVNPTKALCNIVNNKXVHFDLLHEDVSLQYF 276
>pdb|3FMS|A Chain A, Crystal Structure Of Tm0439, A Gntr Transcriptional
Regulator
Length = 209
Score = 29.3 bits (64), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 51/105 (48%), Gaps = 9/105 (8%)
Query: 174 ANVSIIGVYGMGGIGKTTLVKEFVRQASENKLFDRVV-----FSEVSQTPDIKKIQGEI- 227
A ++ V G T + ++F+R+ E ++ V F +++ + ++ +I+GEI
Sbjct: 51 ATEGLVKVVPRVGFFVTDVDEKFIRETIETRIXXEVFCLENYFDKIAGSEELLEIKGEID 110
Query: 228 --AEKLGLELSDEAEYRRASRLYERLKNENKILVILDNIWKHLDL 270
A E+ D+++ R +L+ R I+ + + IW +DL
Sbjct: 111 DVAASAAREIFDDSD-ERLHKLFIRASGNELIISLYEKIWDRIDL 154
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
0.319 0.135 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,462,751
Number of Sequences: 62578
Number of extensions: 868165
Number of successful extensions: 2833
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: 2826
Number of HSP's gapped (non-prelim): 18
length of query: 780
length of database: 14,973,337
effective HSP length: 106
effective length of query: 674
effective length of database: 8,340,069
effective search space: 5621206506
effective search space used: 5621206506
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)