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= 036903
(323 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 62/225 (27%), Positives = 102/225 (45%), Gaps = 52/225 (23%)
Query: 8 LDRFGPGSRIIVTTRDKRVLDNFGVP------NTNIYKVRGLNYSEALELFCNFAFKQSN 61
L F +I++TTRDK V D+ P +++ K +GL E L LF N K+++
Sbjct: 251 LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGL---EILSLFVN--MKKAD 305
Query: 62 CPDGLFTLSKHIVGYCKGNPLALRVLGSFLHRKSKLDWENALENLK----------RSSD 111
P+ + I+ CKG+PL + ++G+ L R WE L+ L+ S D
Sbjct: 306 LPEQAHS----IIKECKGSPLVVSLIGALL-RDFPNRWEYYLKQLQNKQFKRIRKSSSYD 360
Query: 112 FEIYD-VLKISYNELNPEEKSLFLDIACFFAGEDKNLVTKIL--------DDSNYVLNVL 162
+E D + IS L + K + D++ +D + TK+L ++ +L
Sbjct: 361 YEALDEAMSISVEMLREDIKDYYTDLSIL--QKDVKVPTKVLCILWDMETEEVEDILQEF 418
Query: 163 VDKSLLRISRYNK---LQMHDL------------LQEMGREIVRQ 192
V+KSLL R K +HDL LQ++ ++I+ Q
Sbjct: 419 VNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQ 463
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 62/225 (27%), Positives = 102/225 (45%), Gaps = 52/225 (23%)
Query: 8 LDRFGPGSRIIVTTRDKRVLDNFGVP------NTNIYKVRGLNYSEALELFCNFAFKQSN 61
L F +I++TTRDK V D+ P +++ K +GL E L LF N K+++
Sbjct: 257 LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGL---EILSLFVN--MKKAD 311
Query: 62 CPDGLFTLSKHIVGYCKGNPLALRVLGSFLHRKSKLDWENALENLK----------RSSD 111
P+ + I+ CKG+PL + ++G+ L R WE L+ L+ S D
Sbjct: 312 LPEQAHS----IIKECKGSPLVVSLIGALL-RDFPNRWEYYLKQLQNKQFKRIRKSSSYD 366
Query: 112 FEIYD-VLKISYNELNPEEKSLFLDIACFFAGEDKNLVTKIL--------DDSNYVLNVL 162
+E D + IS L + K + D++ +D + TK+L ++ +L
Sbjct: 367 YEALDEAMSISVEMLREDIKDYYTDLS--ILQKDVKVPTKVLCILWDMETEEVEDILQEF 424
Query: 163 VDKSLLRISRYNK---LQMHDL------------LQEMGREIVRQ 192
V+KSLL R K +HDL LQ++ ++I+ Q
Sbjct: 425 VNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQ 469
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 69/264 (26%), Positives = 111/264 (42%), Gaps = 53/264 (20%)
Query: 8 LDRFGPGSRIIVTTRDKRVLDNFGVPNTNIYKVRGLNYSEALELFCNFA-FKQSNCPDGL 66
L F +I++TTRDK V D+ P + GL + LE+ F K+ + P
Sbjct: 251 LKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLP--- 307
Query: 67 FTLSKHIVGYCKGNPLALRVLGSFLHRKSKLDWENALENLK----------RSSDFEIYD 116
+ I+ CKG+PL + ++G+ L R W L L+ S D+E D
Sbjct: 308 -AEAHSIIKECKGSPLVVSLIGALL-RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALD 365
Query: 117 -VLKISYNELNPEEKSLFLDIACFFAGEDKNLVTKIL--------DDSNYVLNVLVDKSL 167
+ IS L + K + D++ +D + TK+L ++ +L V+KSL
Sbjct: 366 EAMSISVEMLREDIKDYYTDLSIL--QKDVKVPTKVLCVLWDLETEEVEDILQEFVNKSL 423
Query: 168 LRISRYNK---LQMHDL------------LQEMGREIVRQ-ESVKEPGKRSRLWDHED-- 209
L +R K +HDL LQ++ R++V Q + +P S D ED
Sbjct: 424 LFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQFQRYYQPHTLSP--DQEDCM 481
Query: 210 ------VYHVLKRNKGTDVIAGIF 227
YH+ N ++ A +F
Sbjct: 482 YWYNFLAYHMASANMHKELCALMF 505
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 68/264 (25%), Positives = 110/264 (41%), Gaps = 53/264 (20%)
Query: 8 LDRFGPGSRIIVTTRDKRVLDNFGVPNTNIYKVRGLNYSEALELFCNFA-FKQSNCPDGL 66
L F +I++TT DK V D+ P + GL + LE+ F K+ + P
Sbjct: 258 LKAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLP--- 314
Query: 67 FTLSKHIVGYCKGNPLALRVLGSFLHRKSKLDWENALENLK----------RSSDFEIYD 116
+ I+ CKG+PL + ++G+ L R W L L+ S D+E D
Sbjct: 315 -AEAHSIIKECKGSPLVVSLIGALL-RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALD 372
Query: 117 -VLKISYNELNPEEKSLFLDIACFFAGEDKNLVTKIL--------DDSNYVLNVLVDKSL 167
+ IS L + K + D++ +D + TK+L ++ +L V+KSL
Sbjct: 373 EAMSISVEMLREDIKDYYTDLSIL--QKDVKVPTKVLCVLWDLETEEVEDILQEFVNKSL 430
Query: 168 LRISRYNK---LQMHDL------------LQEMGREIVRQ-ESVKEPGKRSRLWDHED-- 209
L +R K +HDL LQ++ R++V Q + +P S D ED
Sbjct: 431 LFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQFQRYYQPHTLSP--DQEDCM 488
Query: 210 ------VYHVLKRNKGTDVIAGIF 227
YH+ N ++ A +F
Sbjct: 489 YWYNFLAYHMASANMHKELCALMF 512
>pdb|2C44|A Chain A, Crystal Structure Of E. Coli Tryptophanase
pdb|2C44|B Chain B, Crystal Structure Of E. Coli Tryptophanase
pdb|2C44|C Chain C, Crystal Structure Of E. Coli Tryptophanase
pdb|2C44|D Chain D, Crystal Structure Of E. Coli Tryptophanase
Length = 471
Score = 31.2 bits (69), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 48/98 (48%), Gaps = 12/98 (12%)
Query: 191 RQESVKEPGKRSRLWDHEDVYHVLKRNKGTDVIA-GIFLDLSKIRDIHLGSRAF----EN 245
R+E++ + G L D EDV+ L + GT + + + + + + GSR++ E+
Sbjct: 27 REEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAES 86
Query: 246 MTNLRLLKFYLPNRRGD-------PIMSSKVHLDQGLD 276
+ N+ ++ +P +G P++ K ++GLD
Sbjct: 87 VKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLD 124
>pdb|2V0Y|A Chain A, Crystal Structure Of Apo C298s Tryptophanase From E.Coli
Length = 467
Score = 30.8 bits (68), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 48/98 (48%), Gaps = 12/98 (12%)
Query: 191 RQESVKEPGKRSRLWDHEDVYHVLKRNKGTDVIA-GIFLDLSKIRDIHLGSRAF----EN 245
R+E++ + G L D EDV+ L + GT + + + + + + GSR++ E+
Sbjct: 23 REEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAES 82
Query: 246 MTNLRLLKFYLPNRRGD-------PIMSSKVHLDQGLD 276
+ N+ ++ +P +G P++ K ++GLD
Sbjct: 83 VKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLD 120
>pdb|2OQX|A Chain A, Crystal Structure Of The Apo Form Of E. Coli Tryptophanase
At 1.9 A Resolution
Length = 467
Score = 30.8 bits (68), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 48/98 (48%), Gaps = 12/98 (12%)
Query: 191 RQESVKEPGKRSRLWDHEDVYHVLKRNKGTDVIA-GIFLDLSKIRDIHLGSRAF----EN 245
R+E++ + G L D EDV+ L + GT + + + + + + GSR++ E+
Sbjct: 23 REEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAES 82
Query: 246 MTNLRLLKFYLPNRRGD-------PIMSSKVHLDQGLD 276
+ N+ ++ +P +G P++ K ++GLD
Sbjct: 83 VKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLD 120
>pdb|2VXO|A Chain A, Human Gmp Synthetase In Complex With Xmp
pdb|2VXO|B Chain B, Human Gmp Synthetase In Complex With Xmp
Length = 697
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 65 GLFTLSKHIVGYCKGNPLALRVLGSFLHRKS 95
+FT+ K ++G C G + +V G +H+KS
Sbjct: 96 AIFTIGKPVLGICYGMQMMNKVFGGTVHKKS 126
>pdb|1S4D|A Chain A, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|B Chain B, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|D Chain D, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|E Chain E, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|F Chain F, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|G Chain G, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|H Chain H, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|I Chain I, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|J Chain J, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|K Chain K, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|L Chain L, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|M Chain M, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
Length = 280
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 31/70 (44%)
Query: 42 GLNYSEALELFCNFAFKQSNCPDGLFTLSKHIVGYCKGNPLALRVLGSFLHRKSKLDWEN 101
G + E + CN A Q + ++ V P A+ V+G + ++ LDW
Sbjct: 200 GRSPDEPVAFVCNAATPQQAVLETTLARAEADVAAAGLEPPAIVVVGEVVRLRAALDWIG 259
Query: 102 ALENLKRSSD 111
AL+ K ++D
Sbjct: 260 ALDGRKLAAD 269
>pdb|2VPI|A Chain A, Human Gmp Synthetase - Glutaminase Domain
pdb|2VPI|B Chain B, Human Gmp Synthetase - Glutaminase Domain
Length = 218
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 66 LFTLSKHIVGYCKGNPLALRVLGSFLHRKS 95
+FT+ K ++G C G + +V G +H+KS
Sbjct: 92 IFTIGKPVLGICYGMQMMNKVFGGTVHKKS 121
>pdb|2V1P|A Chain A, Crystal Structure Of The Apo Form Of Y74f Mutant E. Coli
Tryptophanase
Length = 467
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 47/98 (47%), Gaps = 12/98 (12%)
Query: 191 RQESVKEPGKRSRLWDHEDVYHVLKRNKGTDVIA-GIFLDLSKIRDIHLGSRAF----EN 245
R+E++ + G L D EDV+ L + GT + + + + + GSR++ E+
Sbjct: 23 REEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAFSGSRSYYALAES 82
Query: 246 MTNLRLLKFYLPNRRGD-------PIMSSKVHLDQGLD 276
+ N+ ++ +P +G P++ K ++GLD
Sbjct: 83 VKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLD 120
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 228 LDLSKIRDI-HLGSRAFENMTNLRLLKFYLPNRRGDPIMSSKVHLDQ 273
LDL +++ + ++ AFE ++NLR L + N R P ++ + LD+
Sbjct: 165 LDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLREIPNLTPLIKLDE 211
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 0.141 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,002,069
Number of Sequences: 62578
Number of extensions: 424794
Number of successful extensions: 1196
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1189
Number of HSP's gapped (non-prelim): 23
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
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: 51 (24.3 bits)