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= 019538
(339 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2P1J|A Chain A, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
pdb|2P1J|B Chain B, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
Length = 186
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 87/182 (47%), Gaps = 27/182 (14%)
Query: 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGE-NSTFQTLVNPKRQVP--NAHVHGITTDM 184
T +V D ETTG + + IIEI + GG+ + TL+ P R++ ++ + GIT +M
Sbjct: 13 TFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEM 72
Query: 185 VCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFL---INEFSRCSYEVP 241
+ + +E+++P L +++ + VAHNA +FD FL I + +E P
Sbjct: 73 L--ENKRSIEEVLPEFLGFLEDS-------IIVAHNA-NFDYRFLRLWIKKVMGLDWERP 122
Query: 242 NNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQR 301
++DTL LA+ L+K +L S V L + HRA+ D + + R
Sbjct: 123 ----YIDTLALAKSLLKLRSYSLDSVVEKLGLGPF-------RHHRALDDARVTAQVFLR 171
Query: 302 LT 303
Sbjct: 172 FV 173
>pdb|1Y97|A Chain A, The Human Trex2 3' Exonuclease Structure Suggests A
Mechanism For Efficient Non-Processive Dna Catalysis
pdb|1Y97|B Chain B, The Human Trex2 3' Exonuclease Structure Suggests A
Mechanism For Efficient Non-Processive Dna Catalysis
Length = 238
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 37/118 (31%), Positives = 52/118 (44%), Gaps = 7/118 (5%)
Query: 206 SRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLP 265
SRQ G I VAHN +D P L E R +P + + +DTL R L ++
Sbjct: 108 SRQ--AGPICLVAHNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTR 165
Query: 266 SK----VSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFT 319
++ SL +L Y +AH A DV+ L LI +L L+ D RG+
Sbjct: 166 ARGRQGYSLGSLFHRYFRAEPSAAHSAEGDVHTLLLIFLHRAAEL-LAWADEQARGWA 222
>pdb|3CG7|A Chain A, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
pdb|3CG7|B Chain B, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
pdb|3CM5|A Chain A, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Mn
pdb|3CM5|B Chain B, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Mn
pdb|3CM6|A Chain A, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Er
pdb|3CM6|B Chain B, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Er
Length = 308
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 252 LARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRL 302
E+ + G L + ++ + EYY +P +G AH AM D ++ ILQR+
Sbjct: 155 FTNEMDRMGPKELSATTNIGKMNEYYDLPTIGRAHDAMDDCLNIATILQRM 205
>pdb|2IOC|B Chain B, The Crystal Structure Of Trex1 Explains The 3' Nucleotide
Specificity And Reveals A Polyproline Ii Helix For
Protein Partenring
pdb|2IOC|A Chain A, The Crystal Structure Of Trex1 Explains The 3' Nucleotide
Specificity And Reveals A Polyproline Ii Helix For
Protein Partenring
Length = 242
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 192 RMEDLIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDT 249
R +D + ILL RQ +P VAHN +D P L E +R S P + F +D+
Sbjct: 99 RFDDNLAILLRAFLQRQPQP---CCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDS 155
Query: 250 LTLARELMKS---GGSNLPSKVSLQAL--REYYGIPLVGSAHRAMADVNCLSLILQ 300
+ + L ++ G+ SL ++ R Y+ P +H A DV L I Q
Sbjct: 156 IAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPT--DSHTAEGDVLTLLSICQ 209
>pdb|3MXJ|B Chain B, Crystal Structure Of The Mtrex1 Apoprotein
pdb|3MXJ|A Chain A, Crystal Structure Of The Mtrex1 Apoprotein
Length = 242
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 192 RMEDLIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDT 249
R +D + ILL RQ +P VAHN +D P L E +R S P + F +D+
Sbjct: 99 RFDDNLAILLRAFLQRQPQP---CCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDS 155
Query: 250 LTLARELMKS---GGSNLPSKVSLQAL--REYYGIPLVGSAHRAMADVNCLSLILQ 300
+ + L ++ G+ SL ++ R Y+ P +H A DV L I Q
Sbjct: 156 IAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPT--DSHTAEGDVLTLLSICQ 209
>pdb|3MXI|B Chain B, Trex1 3' Exonuclease D18n Familial Chilblain Lupus Mutant
pdb|3MXI|A Chain A, Trex1 3' Exonuclease D18n Familial Chilblain Lupus Mutant
Length = 242
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 192 RMEDLIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDT 249
R +D + ILL RQ +P VAHN +D P L E +R S P + F +D+
Sbjct: 99 RFDDNLAILLRAFLQRQPQP---CCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDS 155
Query: 250 LTLARELMKS---GGSNLPSKVSLQAL--REYYGIPLVGSAHRAMADVNCLSLILQ 300
+ + L ++ G+ SL ++ R Y+ P +H A DV L I Q
Sbjct: 156 IAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPT--DSHTAEGDVLTLLSICQ 209
>pdb|2O4G|A Chain A, Structure Of Trex1 In Complex With A Nucleotide
pdb|2O4G|B Chain B, Structure Of Trex1 In Complex With A Nucleotide
pdb|2O4G|C Chain C, Structure Of Trex1 In Complex With A Nucleotide
pdb|2O4G|D Chain D, Structure Of Trex1 In Complex With A Nucleotide
pdb|3B6O|A Chain A, Structure Of Trex1 In Complex With A Nucleotide And An
Inhibitor Ion (Lithium)
pdb|3B6O|B Chain B, Structure Of Trex1 In Complex With A Nucleotide And An
Inhibitor Ion (Lithium)
pdb|3B6O|C Chain C, Structure Of Trex1 In Complex With A Nucleotide And An
Inhibitor Ion (Lithium)
pdb|3B6O|D Chain D, Structure Of Trex1 In Complex With A Nucleotide And An
Inhibitor Ion (Lithium)
pdb|3B6P|A Chain A, Structure Of Trex1 In Complex With A Nucleotide And
Inhibitor Ions (Sodium And Zinc)
pdb|3B6P|B Chain B, Structure Of Trex1 In Complex With A Nucleotide And
Inhibitor Ions (Sodium And Zinc)
pdb|3B6P|C Chain C, Structure Of Trex1 In Complex With A Nucleotide And
Inhibitor Ions (Sodium And Zinc)
pdb|3B6P|D Chain D, Structure Of Trex1 In Complex With A Nucleotide And
Inhibitor Ions (Sodium And Zinc)
Length = 247
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 192 RMEDLIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDT 249
R +D + ILL RQ +P VAHN +D P L E +R S P + F +D+
Sbjct: 101 RFDDNLAILLRAFLQRQPQP---CCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDS 157
Query: 250 LTLARELMKS---GGSNLPSKVSLQAL--REYYGIPLVGSAHRAMADVNCLSLILQ 300
+ + L ++ G+ SL ++ R Y+ P +H A DV L I Q
Sbjct: 158 IAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPT--DSHTAEGDVLTLLSICQ 211
>pdb|2OA8|A Chain A, Crystal Structure Of Mtrex1 With Ssdna
pdb|2OA8|B Chain B, Crystal Structure Of Mtrex1 With Ssdna
Length = 233
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 192 RMEDLIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDT 249
R +D + ILL RQ +P VAHN +D P L E +R S P + F +D+
Sbjct: 96 RFDDNLAILLRAFLQRQPQP---CCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDS 152
Query: 250 LTLARELMKS---GGSNLPSKVSLQAL--REYYGIPLVGSAHRAMADVNCLSLILQ 300
+ + L ++ G+ SL ++ R Y+ P +H A DV L I Q
Sbjct: 153 IAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPT--DSHTAEGDVLTLLSICQ 206
>pdb|3MXM|B Chain B, Trex1 3' Exonuclease V201d Aicardi-Goutieres Syndrome
Mutant
pdb|3MXM|A Chain A, Trex1 3' Exonuclease V201d Aicardi-Goutieres Syndrome
Mutant
Length = 242
Score = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 192 RMEDLIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDT 249
R +D + ILL RQ +P VAHN +D P L E +R S P + F +D+
Sbjct: 99 RFDDNLAILLRAFLQRQPQP---CCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDS 155
Query: 250 LTLARELMKS 259
+ + L ++
Sbjct: 156 IAALKALEQA 165
>pdb|2O4I|A Chain A, Structure Of Trex1 In Complex With Dna
pdb|2O4I|B Chain B, Structure Of Trex1 In Complex With Dna
Length = 247
Score = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 192 RMEDLIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDT 249
R +D + ILL RQ +P VAHN +D P L E +R S P + F +D+
Sbjct: 101 RFDDNLAILLRAFLQRQPQP---CCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDS 157
Query: 250 LTLARELMKS 259
+ + L ++
Sbjct: 158 IAALKALEQA 167
>pdb|3U6F|B Chain B, Mouse Trex1 D200n Mutant
pdb|3U6F|A Chain A, Mouse Trex1 D200n Mutant
Length = 314
Score = 31.6 bits (70), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 192 RMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDTL 250
R +D + ILL RQ VAHN +D P L E +R S P + F +D++
Sbjct: 99 RFDDNLAILLRAFLQRQP--QPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSI 156
Query: 251 TLARELMKS 259
+ L ++
Sbjct: 157 AALKALEQA 165
>pdb|3U3Y|B Chain B, Mouse Trex1 D200h Mutant
pdb|3U3Y|A Chain A, Mouse Trex1 D200h Mutant
Length = 314
Score = 31.6 bits (70), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 192 RMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF-MDTL 250
R +D + ILL RQ VAHN +D P L E +R S P + F +D++
Sbjct: 99 RFDDNLAILLRAFLQRQP--QPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSI 156
Query: 251 TLARELMKS 259
+ L ++
Sbjct: 157 AALKALEQA 165
>pdb|4G65|A Chain A, Potassium Transporter Peripheral Membrane Component (Trka)
From Vibrio Vulnificus
pdb|4G65|B Chain B, Potassium Transporter Peripheral Membrane Component (Trka)
From Vibrio Vulnificus
Length = 461
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 267 KVSLQALREYYGIPLVGSAHRAM 289
KVSL A++ YYG PLVG+A A+
Sbjct: 155 KVSLVAVKAYYGGPLVGNALSAL 177
>pdb|1V7L|A Chain A, Structure Of 3-Isopropylmalate Isomerase Small Subunit
From Pyrococcus Horikoshii
pdb|1V7L|B Chain B, Structure Of 3-Isopropylmalate Isomerase Small Subunit
From Pyrococcus Horikoshii
Length = 163
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 21/53 (39%)
Query: 20 SLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTERWSRRRITTGTE 72
+A ESF R + LL KT GL+D D T W + G E
Sbjct: 78 GIAGVIAESFGRIFYRNAINIGIPLLLGKTEGLKDGDLVTVNWETGEVRKGDE 130
>pdb|1JQO|A Chain A, Crystal Structure Of C4-Form Phosphoenolpyruvate
Carboxylase From Maize
pdb|1JQO|B Chain B, Crystal Structure Of C4-Form Phosphoenolpyruvate
Carboxylase From Maize
Length = 970
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 253 ARELMKSGGSNLPSKVSLQALREYYGI------PLVGSAHRAMADVNCLSLILQRLTFDL 306
AR L+ SG S + ++ S ++ E+ L +A+AD + L L+ Q TF L
Sbjct: 389 ARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGL 448
Query: 307 KLSLCDLIERGFTPSDLIN 325
L D+ + +D+I+
Sbjct: 449 SLVKLDIRQESERHTDVID 467
>pdb|2GH8|A Chain A, X-Ray Structure Of A Native Calicivirus
pdb|2GH8|B Chain B, X-Ray Structure Of A Native Calicivirus
pdb|2GH8|C Chain C, X-Ray Structure Of A Native Calicivirus
Length = 558
Score = 27.7 bits (60), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 19/43 (44%)
Query: 132 FDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPN 174
FD TTG+S IEI Q +G N F + K VP
Sbjct: 256 FDSTTTGWSTPYYVPIEIKIQGKVGSNNKWFHVIDTDKALVPG 298
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 0.136 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,588,671
Number of Sequences: 62578
Number of extensions: 381348
Number of successful extensions: 886
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: 878
Number of HSP's gapped (non-prelim): 18
length of query: 339
length of database: 14,973,337
effective HSP length: 99
effective length of query: 240
effective length of database: 8,778,115
effective search space: 2106747600
effective search space used: 2106747600
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: 52 (24.6 bits)