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= 039944
(348 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 35/114 (30%), Positives = 57/114 (50%), Gaps = 12/114 (10%)
Query: 66 EHLEIISCPSLTCIFSK-NELPATLESLEVGNLPLSLKSLFVYGCSKLGSIAERLDNNTS 124
EH +++ SL ++ LPA++ +L+ +LKSL + S L ++ + +
Sbjct: 178 EHQGLVNLQSLRLEWTGIRSLPASIANLQ------NLKSLKIRN-SPLSALGPAIHHLPK 230
Query: 125 LETISIDSCGNLVSFPE--GGLPCAKLTRLTILDCKRLEALPKGMHNLTSLQYL 176
LE + + C L ++P GG A L RL + DC L LP +H LT L+ L
Sbjct: 231 LEELDLRGCTALRNYPPIFGGR--APLKRLILKDCSNLLTLPLDIHRLTQLEKL 282
>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With
An 8-Base Single-Stranded Dna Oligonucleotide
Length = 659
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 214 ERGRGFHRFSSLRRLTISRCD-EDMVSFPLEDKRLGTALPLPASLTSLWIEAFPNLERLS 272
E GR HR L ++R + + DKR + PLP SL++L IEA +
Sbjct: 252 EEGRLLHR--PLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSA 309
Query: 273 SSIVDL-QNLTE---LYLFGCPKLKYFPEK 298
+++D+ Q L E L F +Y PE+
Sbjct: 310 QNVLDICQKLYETHKLITFPRSDCRYLPEE 339
>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O19|B Chain B, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O54|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O54|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O59|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O59|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O5C|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5C|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5E|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
pdb|2O5E|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
Length = 659
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 7/90 (7%)
Query: 214 ERGRGFHRFSSLRRLTISRCD-EDMVSFPLEDKRLGTALPLPASLTSLWIEAFPNLERLS 272
E GR HR L ++R + + DKR + PLP SL++L IEA +
Sbjct: 252 EEGRLLHR--PLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSA 309
Query: 273 SSIVDL-QNLTELY-LFGCPK--LKYFPEK 298
+++D+ Q L E + L P+ +Y PE+
Sbjct: 310 QNVLDICQKLYETHKLITYPRSDCRYLPEE 339
>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
Length = 653
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 7/90 (7%)
Query: 214 ERGRGFHRFSSLRRLTISRCD-EDMVSFPLEDKRLGTALPLPASLTSLWIEAFPNLERLS 272
E GR HR L ++R + + DKR + PLP SL++L IEA +
Sbjct: 252 EEGRLLHR--PLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSA 309
Query: 273 SSIVDL-QNLTELY-LFGCPK--LKYFPEK 298
+++D+ Q L E + L P+ +Y PE+
Sbjct: 310 QNVLDICQKLYETHKLITYPRSDCRYLPEE 339
>pdb|3SF6|A Chain A, Crystal Structure Of Glutaryl-Coa Dehydrogenase From
Mycobacterium Smegmatis
Length = 403
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 74 PSLTCIFSKNELPATLESLEVGNLPLSLKSLFVYGCSKLGSIA 116
P + + ELPA ++E+G L L L YGC+ + ++A
Sbjct: 51 PHIASWYEDGELPARELAVELGELGLLGMHLKGYGCAGMSAVA 93
>pdb|3UFB|A Chain A, Crystal Structure Of A Modification Subunit Of A Putative
Type I Restriction Enzyme From Vibrio Vulnificus Yj016
Length = 530
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 49/194 (25%), Positives = 80/194 (41%), Gaps = 37/194 (19%)
Query: 141 EGGLPCAKLTRLTILDCKRLEAL-PKGMHNLTSLQYLRIGKGGALPSLEEEDGLPTNLQS 199
EGG+ +L D EA+ P G + YLR +G + D + T +
Sbjct: 93 EGGITGDELIAFINND----EAMRPDGTRGIGLFAYLRSLQGDN--GGDRRDVIATVFKG 146
Query: 200 L-DIWGNMEIWKSMIERGRGFHRFSSLRRLTISRCDEDM--------------------V 238
+ + N + + ++++ G H SS T+SR E M V
Sbjct: 147 MQNRMINGYLLRDVVDKINGIHFNSSEEMHTLSRLYETMLREMRDAAGDSGEFYTPRPVV 206
Query: 239 SFPLE--DKRLGTALPLPASLTS-LWIEAFPNLERLSSSIVDLQNLTELYLFGCPKLKYF 295
F +E D +LG ++ PA T +EAF +LER ++ D + L E +FG
Sbjct: 207 RFMVEVMDPQLGESVLDPACGTGGFLVEAFEHLERQCKTVEDREVLQESSIFGGEA---- 262
Query: 296 PEKGLPSSLLELRI 309
K LP L+++ +
Sbjct: 263 --KSLPYLLVQMNL 274
>pdb|1M6V|B Chain B, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
pdb|1M6V|D Chain D, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
pdb|1M6V|F Chain F, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
pdb|1M6V|H Chain H, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
Length = 382
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 182 GALPSLEEEDGLPTNLQSLDIWGNMEIWKSMIERG 216
G LP ++ED LP ++ + D I + +++RG
Sbjct: 179 GGLPQAKKEDELPFHVVAYDFGAKRNILRMLVDRG 213
>pdb|1JDB|C Chain C, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1JDB|F Chain F, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1JDB|I Chain I, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1JDB|L Chain L, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1BXR|B Chain B, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1BXR|D Chain D, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1BXR|F Chain F, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1BXR|H Chain H, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1CE8|B Chain B, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
pdb|1CE8|D Chain D, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
pdb|1CE8|F Chain F, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
pdb|1CE8|H Chain H, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
Length = 382
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 182 GALPSLEEEDGLPTNLQSLDIWGNMEIWKSMIERG 216
G LP ++ED LP ++ + D I + +++RG
Sbjct: 179 GGLPQAKKEDELPFHVVAYDFGAKRNILRMLVDRG 213
>pdb|1A9X|B Chain B, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
pdb|1A9X|D Chain D, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
pdb|1A9X|F Chain F, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
pdb|1A9X|H Chain H, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
Length = 379
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 182 GALPSLEEEDGLPTNLQSLDIWGNMEIWKSMIERG 216
G LP ++ED LP ++ + D I + +++RG
Sbjct: 178 GGLPQAKKEDELPFHVVAYDFGAKRNILRMLVDRG 212
>pdb|1C30|B Chain B, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C30|D Chain D, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C30|F Chain F, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C30|H Chain H, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C3O|B Chain B, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
pdb|1C3O|D Chain D, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
pdb|1C3O|F Chain F, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
pdb|1C3O|H Chain H, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
Length = 382
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 182 GALPSLEEEDGLPTNLQSLDIWGNMEIWKSMIERG 216
G LP ++ED LP ++ + D I + +++RG
Sbjct: 179 GGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRG 213
>pdb|1CS0|B Chain B, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1CS0|D Chain D, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1CS0|F Chain F, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1CS0|H Chain H, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1KEE|B Chain B, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
pdb|1KEE|D Chain D, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
pdb|1KEE|F Chain F, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
pdb|1KEE|H Chain H, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
Length = 382
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 182 GALPSLEEEDGLPTNLQSLDIWGNMEIWKSMIERG 216
G LP ++ED LP ++ + D I + +++RG
Sbjct: 179 GGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRG 213
>pdb|1T36|B Chain B, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
pdb|1T36|D Chain D, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
pdb|1T36|F Chain F, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
pdb|1T36|H Chain H, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
Length = 382
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 182 GALPSLEEEDGLPTNLQSLDIWGNMEIWKSMIERG 216
G LP ++ED LP ++ + D I + +++RG
Sbjct: 179 GGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRG 213
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 27.7 bits (60), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 19/94 (20%)
Query: 263 EAFPNLERLSSSIVDLQNLTELYLFGCPKLKYFPEKG------------LPSSLLELRIS 310
E +P + R + I + +N+T +L G P + EKG L S++E++
Sbjct: 59 EFYP-IYRDLTKIREKRNITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTD 117
Query: 311 RCPL-IAEKCRKDGGQ-----YWDLLTHIPRVEI 338
PL + +K +KDG Q Y+ LL + + ++
Sbjct: 118 DSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADV 151
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 0.138 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,956,630
Number of Sequences: 62578
Number of extensions: 397406
Number of successful extensions: 745
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 728
Number of HSP's gapped (non-prelim): 25
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
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: 52 (24.6 bits)