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= 003403
(823 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GF3|A Chain A, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Co-Crystallized With Glutaconyl-Coa
pdb|3GF7|A Chain A, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Apoprotein
pdb|3GLM|A Chain A, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Co-Crystallized With Crotonyl-Coa
pdb|3GLM|B Chain B, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Co-Crystallized With Crotonyl-Coa
pdb|3GLM|C Chain C, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Co-Crystallized With Crotonyl-Coa
pdb|3GLM|D Chain D, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Co-Crystallized With Crotonyl-Coa
pdb|3GMA|A Chain A, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Co-Crystallized With Glutaryl-Coa
pdb|3GMA|B Chain B, Glutaconyl-Coa Decarboxylase A Subunit From Clostridium
Symbiosum Co-Crystallized With Glutaryl-Coa
Length = 588
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 162 LGALASVVAMLLPYPRLAYHEVKKSSKLYAENASEMLNHFVKAFCAQD--------NTAA 213
+G +A+V +L+ YP + V KLY + +M N FV CA+D +T
Sbjct: 362 VGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKM-NEFV-TLCARDRIPLIWLQDTTG 419
Query: 214 LDSISEAK--SLFKAGAKQLLSIKDKQ 238
+D EA+ L G + SI++ +
Sbjct: 420 IDVGDEAEKAELLGLGQSLIYSIENSK 446
>pdb|2CJQ|A Chain A, Bovine Viral Diarrhea Virus Cp7-R12 Rna-Dependent Rna
Polymerase
Length = 720
Score = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 49/113 (43%), Gaps = 15/113 (13%)
Query: 666 VSWKQIQEPINDDLE---LFKEKVGHSLKCFEEVI--LIKSLAV---------LAPERQN 711
V+W+Q++ +N L K+ VG L + ++ LI+ L P+ +
Sbjct: 207 VTWEQLEAGVNRKGAAGFLEKKNVGEVLDSEKHLVEQLIRDLKTGRKIRYYETAIPKNEK 266
Query: 712 RNISHDVESGRLPNEDVPRTLS-PDXXXXXXXLSSFLQHSKEVANSINGYDGE 763
R++S D +SG L +E PR + P+ K+ I GY+G+
Sbjct: 267 RDVSDDWQSGDLVDEKKPRVIQYPEAKTRLAITKVMYNWVKQQPVVIPGYEGK 319
>pdb|1AOS|A Chain A, Human Argininosuccinate Lyase
pdb|1AOS|B Chain B, Human Argininosuccinate Lyase
Length = 464
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 48/99 (48%), Gaps = 12/99 (12%)
Query: 625 FLPFHGSCYENILASLSRMA-DLLLFVAYKTEFLSQLSERFGVSWKQIQEPIN-DDLELF 682
FL + C + LSRMA DL+L+ + F+ QLS+ + + + N D LEL
Sbjct: 242 FLFWRSLC----MTHLSRMAEDLILYCTKEFSFV-QLSDAYSTGSSLMPQKKNPDSLELI 296
Query: 683 KEKVGHSL-KCFEEVILIKSLAVLAPERQNRNISHDVES 720
+ K G +C ++ +K L P N+++ D E+
Sbjct: 297 RSKAGRVFGRCAGLLMTLKGL----PSTYNKDLQEDKEA 331
>pdb|3RW9|A Chain A, Crystal Structure Of Human Spermidine Synthase In Complex
With Decarboxylated S-Adenosylhomocysteine
pdb|3RW9|B Chain B, Crystal Structure Of Human Spermidine Synthase In Complex
With Decarboxylated S-Adenosylhomocysteine
Length = 304
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 211 TAALDSISEAKSLFKAGAKQLLSIKDKQEGMLWERPQIRFLKPNY-KDPREKLQELEIPI 269
T + D + A+SLFK QL+ K++G+L + + ++L + K+ R+ Q L P+
Sbjct: 174 TDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSL-FPV 232
Query: 270 RGMELALTSCPSFPVGMI 287
+ A + P++P G I
Sbjct: 233 --VAYAYCTIPTYPSGQI 248
>pdb|2O05|A Chain A, Human Spermidine Synthase
pdb|2O05|B Chain B, Human Spermidine Synthase
pdb|2O06|A Chain A, Human Spermidine Synthase
pdb|2O06|B Chain B, Human Spermidine Synthase
pdb|2O07|A Chain A, Human Spermidine Synthase
pdb|2O07|B Chain B, Human Spermidine Synthase
pdb|2O0L|A Chain A, Human Spermidine Synthase
pdb|2O0L|B Chain B, Human Spermidine Synthase
Length = 304
Score = 29.6 bits (65), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 211 TAALDSISEAKSLFKAGAKQLLSIKDKQEGMLWERPQIRFLKPNY-KDPREKLQELEIPI 269
T + D + A+SLFK QL+ K++G+L + + ++L + K+ R+ Q L P+
Sbjct: 174 TDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSL-FPV 232
Query: 270 RGMELALTSCPSFPVGMI 287
+ A + P++P G I
Sbjct: 233 --VAYAYCTIPTYPSGQI 248
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 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,744,895
Number of Sequences: 62578
Number of extensions: 752362
Number of successful extensions: 1529
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1527
Number of HSP's gapped (non-prelim): 9
length of query: 823
length of database: 14,973,337
effective HSP length: 107
effective length of query: 716
effective length of database: 8,277,491
effective search space: 5926683556
effective search space used: 5926683556
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: 56 (26.2 bits)