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= 001860
(1003 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 54/251 (21%), Positives = 97/251 (38%), Gaps = 55/251 (21%)
Query: 159 TLKEILDALSNRKFNMIG------VYGMGGVGKTTLVKEVGRKAKENKLFEKVISAHV-- 210
T K+++ A+ + + + G +YGM G GK+ L E R ++ L E S V
Sbjct: 135 TRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVR---DHSLLEGCFSGGVHW 191
Query: 211 ------SRTPQIKKIQE-----EIAEKMGLRLVEEIETVRAGRLYERLKVEKKILIILDD 259
++ + K+Q + E RL IE + L+ + L+ILDD
Sbjct: 192 VSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDD 251
Query: 260 IWGSLDLEAIG------------------------IPLADD---NSGREAWSLFTKTTGD 292
+W L+A +P+ G E SLF
Sbjct: 252 VWDPWVLKAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVN---- 307
Query: 293 CIENDELRSVAKDIVKECAGLPIAIVPVARALRNKRLCEWKDALLELRRPSLRNFSGTLE 352
++ ++L + A I+KEC G P+ + + LR+ W L +L+ + +
Sbjct: 308 -MKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFKRIRKSSS 365
Query: 353 VAYKSIELSYS 363
Y++++ + S
Sbjct: 366 YDYEALDEAMS 376
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 54/251 (21%), Positives = 97/251 (38%), Gaps = 55/251 (21%)
Query: 159 TLKEILDALSNRKFNMIG------VYGMGGVGKTTLVKEVGRKAKENKLFEKVISAHV-- 210
T K+++ A+ + + + G +YGM G GK+ L E R ++ L E S V
Sbjct: 128 TRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVR---DHSLLEGCFSGGVHW 184
Query: 211 ------SRTPQIKKIQE-----EIAEKMGLRLVEEIETVRAGRLYERLKVEKKILIILDD 259
++ + K+Q + E RL IE + L+ + L+ILDD
Sbjct: 185 VSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDD 244
Query: 260 IWGSLDLEAIG------------------------IPLADD---NSGREAWSLFTKTTGD 292
+W L+A +P+ G E SLF
Sbjct: 245 VWDPWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVN---- 300
Query: 293 CIENDELRSVAKDIVKECAGLPIAIVPVARALRNKRLCEWKDALLELRRPSLRNFSGTLE 352
++ ++L + A I+KEC G P+ + + LR+ W L +L+ + +
Sbjct: 301 -MKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFKRIRKSSS 358
Query: 353 VAYKSIELSYS 363
Y++++ + S
Sbjct: 359 YDYEALDEAMS 369
>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 = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 80/348 (22%), Positives = 136/348 (39%), Gaps = 67/348 (19%)
Query: 138 IPEEPWLKSTQGFVHFQSRKCTLKEILDALSNRKF--NMIGVYGMGGVGKTTLVKEVGRK 195
+P+ P V F +RK + I LS K + ++GM G GK+ L E R
Sbjct: 125 VPQRP--------VVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVR- 175
Query: 196 AKENKLFEKVISAHV--------SRTPQIKKIQE-----EIAEKMGLRLVEEIETVRAGR 242
++ L E V ++ + K+Q + E RL IE +
Sbjct: 176 --DHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRL 233
Query: 243 LYERLKVEKKILIILDDIWGSLDLEAIG------------------------IPLADD-- 276
L+ + L+ILDD+W S L+A +P+
Sbjct: 234 RILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 293
Query: 277 -NSGREAWSLFTKTTGDCIENDELRSVAKDIVKECAGLPIAIVPVARALRNKRLCEWKDA 335
G E SLF ++ +L A I+KEC G P+ + + LR+ W+
Sbjct: 294 KEKGLEILSLFVN-----MKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYY 347
Query: 336 LLELRRPSLRNFSGTLEVAYKSIELSYSHLNGEELKSTFLLIRYAFISCVE-DVLFSGMG 394
L +L+ + + Y++++ + S ++ E L+ + Y +S ++ DV
Sbjct: 348 LKQLQNKQFKRIRKSSSYDYEALDEAMS-ISVEMLRED-IKDYYTDLSILQKDVKVPTKV 405
Query: 395 LGLFQNINTLEEARDRAHTLVENLKKSCLLLDGNTSEW-FSMHDVVRD 441
L + ++ T EE D L E + KS L D N + + +HD+ D
Sbjct: 406 LCILWDMET-EEVED---ILQEFVNKSLLFCDRNGKSFRYYLHDLQVD 449
>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 = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 80/348 (22%), Positives = 136/348 (39%), Gaps = 67/348 (19%)
Query: 138 IPEEPWLKSTQGFVHFQSRKCTLKEILDALSNRKF--NMIGVYGMGGVGKTTLVKEVGRK 195
+P+ P V F +RK + I LS K + ++GM G GK+ L E R
Sbjct: 119 VPQRP--------VVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVR- 169
Query: 196 AKENKLFEKVISAHV--------SRTPQIKKIQE-----EIAEKMGLRLVEEIETVRAGR 242
++ L E V ++ + K+Q + E RL IE +
Sbjct: 170 --DHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRL 227
Query: 243 LYERLKVEKKILIILDDIWGSLDLEAIG------------------------IPLADD-- 276
L+ + L+ILDD+W S L+A +P+
Sbjct: 228 RILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 287
Query: 277 -NSGREAWSLFTKTTGDCIENDELRSVAKDIVKECAGLPIAIVPVARALRNKRLCEWKDA 335
G E SLF ++ +L A I+KEC G P+ + + LR+ W+
Sbjct: 288 KEKGLEILSLFVN-----MKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYY 341
Query: 336 LLELRRPSLRNFSGTLEVAYKSIELSYSHLNGEELKSTFLLIRYAFISCVE-DVLFSGMG 394
L +L+ + + Y++++ + S ++ E L+ + Y +S ++ DV
Sbjct: 342 LKQLQNKQFKRIRKSSSYDYEALDEAMS-ISVEMLRED-IKDYYTDLSILQKDVKVPTKV 399
Query: 395 LGLFQNINTLEEARDRAHTLVENLKKSCLLLDGNTSEW-FSMHDVVRD 441
L + ++ T EE D L E + KS L D N + + +HD+ D
Sbjct: 400 LCILWDMET-EEVED---ILQEFVNKSLLFCDRNGKSFRYYLHDLQVD 443
>pdb|2V1U|A Chain A, Structure Of The Aeropyrum Pernix Orc1 Protein In Complex
With Dna
Length = 387
Score = 33.5 bits (75), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 60/121 (49%), Gaps = 16/121 (13%)
Query: 152 HFQSRKCTLKEIL-DALSNRKFNMIGVYGMGGVGKTTLVKEVGRK--AKENKLFEKV--- 205
H ++ L E+L AL K + +YG+ G GKT + + V R+ A+ + L V
Sbjct: 23 HREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPI 82
Query: 206 -ISAHVSRTPQIKKIQEEIAEKMGLRLVEEIETVRAGRLYERL-----KVEKKILIILDD 259
++A TP ++ IAE +G+R+ + G +YERL ++ +I+LD+
Sbjct: 83 YVNARHRETPY--RVASAIAEAVGVRV--PFTGLSVGEVYERLVKRLSRLRGIYIIVLDE 138
Query: 260 I 260
I
Sbjct: 139 I 139
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 33.1 bits (74), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 33/99 (33%), Positives = 49/99 (49%), Gaps = 6/99 (6%)
Query: 563 LKKLEILTL-RGSNMQKLVEEIGRLTQLRLLDLSNCSKLKVIPANVISSLSRIEELYIGE 621
L LE+L L R S Q V L L L+L + + L VIP+ LS++ EL++
Sbjct: 98 LHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFD-NWLTVIPSGAFEYLSKLRELWLRN 156
Query: 622 SPIEWVKVEGIDGERRNASLHELNHLSKLTSLEILIQDA 660
+PIE + + R SL L+ L +L LE + + A
Sbjct: 157 NPIESIPSYAFN---RVPSLMRLD-LGELKKLEYISEGA 191
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 32.3 bits (72), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 51/99 (51%), Gaps = 6/99 (6%)
Query: 563 LKKLEILTLRGSNMQKL-VEEIGRLTQLRLLDLSNCSKLKVIPANVISSLSRIEELYIGE 621
L+ LEIL L + ++K+ V L L L+L + ++L +P LS++ EL++
Sbjct: 58 LRHLEILQLSKNLVRKIEVGAFNGLPSLNTLELFD-NRLTTVPTQAFEYLSKLRELWLRN 116
Query: 622 SPIEWVKVEGIDGERRNASLHELNHLSKLTSLEILIQDA 660
+PIE + + R SL L+ L +L LE + + A
Sbjct: 117 NPIESIPSYAFN---RVPSLRRLD-LGELKRLEYISEAA 151
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 51/99 (51%), Gaps = 6/99 (6%)
Query: 563 LKKLEILTLRGSNMQKL-VEEIGRLTQLRLLDLSNCSKLKVIPANVISSLSRIEELYIGE 621
L+ LEIL L + ++K+ V L L L+L + ++L +P LS++ EL++
Sbjct: 58 LRHLEILQLSKNLVRKIEVGAFNGLPSLNTLELFD-NRLTTVPTQAFEYLSKLRELWLRN 116
Query: 622 SPIEWVKVEGIDGERRNASLHELNHLSKLTSLEILIQDA 660
+PIE + + R SL L+ L +L LE + + A
Sbjct: 117 NPIESIPSYAFN---RVPSLRRLD-LGELKRLEYISEAA 151
>pdb|2NN5|A Chain A, Structure Of Conserved Protein Of Unknown Function Ef2215
From Enterococcus Faecalis
Length = 184
Score = 31.6 bits (70), Expect = 2.5, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 760 VVDTMDCTPARTAFPLLESLFLKDLSNLE 788
VV+T D P + FP +E+ +L+ L+NLE
Sbjct: 155 VVETPDAAPEKIDFPQIENHYLEKLTNLE 183
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 49/94 (52%), Gaps = 8/94 (8%)
Query: 563 LKKLEILTLRGSNMQKLVEEIGR---LTQLRLLDLSNCSKLKVIPANVISSLSRIEELYI 619
L+ LEIL L ++++ + EIG L L L+L + ++L IP LS+++EL++
Sbjct: 87 LRHLEILQLSRNHIRTI--EIGAFNGLANLNTLELFD-NRLTTIPNGAFVYLSKLKELWL 143
Query: 620 GESPIEWVKVEGID--GERRNASLHELNHLSKLT 651
+PIE + + R L EL LS ++
Sbjct: 144 RNNPIESIPSYAFNRIPSLRRLDLGELKRLSYIS 177
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 30.8 bits (68), Expect = 3.5, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 559 IIGDLKKLEILTLRG-SNMQKLVEEIGRLTQLRLLDLSNCSKLKVIPA 605
I G L+ L L+ SN+ L +I RLTQL LDL C L +P+
Sbjct: 248 IFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPS 295
>pdb|2B8N|A Chain A, Crystal Structure Of Glycerate Kinase (ec 2.7.1.31)
(tm1585) From Thermotoga Maritima At 2.70 A Resolution
pdb|2B8N|B Chain B, Crystal Structure Of Glycerate Kinase (ec 2.7.1.31)
(tm1585) From Thermotoga Maritima At 2.70 A Resolution
Length = 429
Score = 30.8 bits (68), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 13/87 (14%)
Query: 232 VEEIETVR-------AGRLYERLKVEKKILIILDDIWGS-LDLEAIGIPLADDNSGREAW 283
+EEI TVR GR ER+ K + ++L D+ G LD+ A G D ++ +A
Sbjct: 167 IEEINTVRKHLSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDAL 226
Query: 284 SLFTKTTGDCIENDELRSVAKDIVKEC 310
+ K IE E SV + I++E
Sbjct: 227 KVLEKY---GIETSE--SVKRAILQET 248
>pdb|3CTV|A Chain A, Crystal Structure Of Central Domain Of 3-Hydroxyacyl-Coa
Dehydrogenase From Archaeoglobus Fulgidus
Length = 110
Score = 30.8 bits (68), Expect = 4.1, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 215 QIKKIQEEIAEKMGLRLVEEIETVRAGRLYERLKVEK 251
QI K EE+A++ G ++ E +T++ G+L E LK K
Sbjct: 70 QIAKRLEELAKQFGKKIFEPAKTLKEGKLEELLKAGK 106
>pdb|2XXA|A Chain A, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
pdb|2XXA|C Chain C, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
Length = 433
Score = 30.0 bits (66), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 177 VYGMGGVGKTTLVKEVGRKAKE-NKLFEKVISAHVSRTPQIKKIQEEIAEKMGL 229
+ G+ G GKTT V ++G+ +E +K V+SA V R IK++ E +AE++G+
Sbjct: 105 MAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQL-ETLAEQVGV 157
>pdb|2Z7Q|A Chain A, Crystal Structure Of The N-Terminal Kinase Domain Of Human
Rsk-1 Bound To Amp-Pcp
pdb|2Z7R|A Chain A, Crystal Structure Of The N-Terminal Kinase Domain Of Human
Rsk1 Bound To Staurosporine
pdb|2Z7S|A Chain A, Crystal Structure Of The N-Terminal Kinase Domain Of Human
Rsk1 Bound To Purvalnol A
Length = 321
Score = 30.0 bits (66), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 172 FNMIGVYGMGGVGKTTLVKEVGRKAKENKLFEKVISAHVSRTPQIKKIQEEIAEKMGLRL 231
F ++ V G G GK LV++V R + KV+ K+++ + KM +
Sbjct: 30 FELLKVLGQGSFGKVFLVRKVTRPDSGHLYAMKVLKK------ATLKVRDRVRTKMERDI 83
Query: 232 VEEIETVRAGRLYERLKVEKKILIILDDIWG 262
+ ++ +L+ + E K+ +ILD + G
Sbjct: 84 LADVNHPFVVKLHYAFQTEGKLYLILDFLRG 114
>pdb|2J28|9 Chain 9, Model Of E. Coli Srp Bound To 70s Rncs
Length = 430
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 177 VYGMGGVGKTTLVKEVGRKAKE-NKLFEKVISAHVSRTPQIKKIQEEIAEKMGL 229
+ G+ G GKTT V ++G+ +E +K V+SA V R IK++ E +AE++G+
Sbjct: 104 MAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQL-ETLAEQVGV 156
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 0.137 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,314,154
Number of Sequences: 62578
Number of extensions: 1164870
Number of successful extensions: 2973
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 2953
Number of HSP's gapped (non-prelim): 49
length of query: 1003
length of database: 14,973,337
effective HSP length: 108
effective length of query: 895
effective length of database: 8,214,913
effective search space: 7352347135
effective search space used: 7352347135
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: 56 (26.2 bits)