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= 035566
(238 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NUQ|A Chain A, Structure Of A Putative Nucleotide Phosphatase From
Saccharomyces Cerevisiae
Length = 282
Score = 70.1 bits (170), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 56/196 (28%), Positives = 92/196 (46%), Gaps = 19/196 (9%)
Query: 5 ECLLFDVDDTLYSHSYGFSNKCSKNIEEYMIQKLGIEESEVSEFNRVLYKNYGTSMAGLK 64
+ FD+D+ LY S + ++I + L + + N YK YG ++ GL
Sbjct: 58 KVFFFDIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGL- 116
Query: 65 AVGYDFDNDDYHSFVHGRLPYEN-LKPDPVLRNLLLSL----PIRKV-IFSNADEIHVAK 118
+ + + +Y+ V LP ++ LKPD LRN+LL L I K+ +F+NA + H +
Sbjct: 117 VMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIR 176
Query: 119 VLRKLGLEDCFDGIVNFE-------SLNPTNKTTGQELQLISMLRMVAHHFFQRLFFDDS 171
LR LG+ D FDG+ + P K + ++ + R + F DDS
Sbjct: 177 CLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLAR-----YENAYFIDDS 231
Query: 172 TRNIECGKSIGLHTVL 187
+NIE G +G+ T +
Sbjct: 232 GKNIETGIKLGMKTCI 247
>pdb|3ONN|A Chain A, Crystal Structure Of 5'-Nucleotidase Sdt1 From
Saccharomyces Cerevisiae
Length = 263
Score = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 56/196 (28%), Positives = 92/196 (46%), Gaps = 19/196 (9%)
Query: 5 ECLLFDVDDTLYSHSYGFSNKCSKNIEEYMIQKLGIEESEVSEFNRVLYKNYGTSMAGLK 64
+ FD+D+ LY S + ++I + L + + N YK YG ++ GL
Sbjct: 31 KVFFFDIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGL- 89
Query: 65 AVGYDFDNDDYHSFVHGRLPYEN-LKPDPVLRNLLLSL----PIRKV-IFSNADEIHVAK 118
+ + + +Y+ V LP ++ LKPD LRN+LL L I K+ +F+NA + H +
Sbjct: 90 VMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIR 149
Query: 119 VLRKLGLEDCFDGIVNFE-------SLNPTNKTTGQELQLISMLRMVAHHFFQRLFFDDS 171
LR LG+ D FDG+ + P K + ++ + R + F DDS
Sbjct: 150 CLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLAR-----YENAYFIDDS 204
Query: 172 TRNIECGKSIGLHTVL 187
+NIE G +G+ T +
Sbjct: 205 GKNIETGIKLGMKTCI 220
>pdb|3OPX|A Chain A, Crystal Structure Of Pyrimidine 5 -Nucleotidase Sdt1 From
Saccharomyces Cerevisiae Complexed With Uridine
5'-Monophosphate
Length = 263
Score = 67.0 bits (162), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 55/196 (28%), Positives = 91/196 (46%), Gaps = 19/196 (9%)
Query: 5 ECLLFDVDDTLYSHSYGFSNKCSKNIEEYMIQKLGIEESEVSEFNRVLYKNYGTSMAGLK 64
+ F +D+ LY S + ++I + L + + N YK YG ++ GL
Sbjct: 31 KVFFFAIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGL- 89
Query: 65 AVGYDFDNDDYHSFVHGRLPYEN-LKPDPVLRNLLLSL----PIRKV-IFSNADEIHVAK 118
+ + + +Y+ V LP ++ LKPD LRN+LL L I K+ +F+NA + H +
Sbjct: 90 VMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIR 149
Query: 119 VLRKLGLEDCFDGIVNFE-------SLNPTNKTTGQELQLISMLRMVAHHFFQRLFFDDS 171
LR LG+ D FDG+ + P K + ++ + R + F DDS
Sbjct: 150 CLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLAR-----YENAYFIDDS 204
Query: 172 TRNIECGKSIGLHTVL 187
+NIE G +G+ T +
Sbjct: 205 GKNIETGIKLGMKTCI 220
>pdb|1QQ5|A Chain A, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus
pdb|1QQ5|B Chain B, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus
Length = 253
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 85 YENLKPDPVLRNLLLSL-PIRKVIFSNADEIHVAKVLRKLGLEDCFDGIVNFES 137
Y L P P L L P+++ I SN + ++ GL D FD +++ ++
Sbjct: 89 YNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDA 142
>pdb|1QQ7|A Chain A, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus With Chloropropionic Acid Covalently Bound
pdb|1QQ7|B Chain B, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus With Chloropropionic Acid Covalently Bound
pdb|1QQ6|A Chain A, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus With Chloroacetic Acid Covalently Bound
pdb|1QQ6|B Chain B, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus With Chloroacetic Acid Covalently Bound
Length = 253
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 85 YENLKPDPVLRNLLLSL-PIRKVIFSNADEIHVAKVLRKLGLEDCFDGIVNFES 137
Y L P P L L P+++ I SN + ++ GL D FD +++ ++
Sbjct: 89 YNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDA 142
>pdb|1AQ6|A Chain A, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus
pdb|1AQ6|B Chain B, Structure Of L-2-Haloacid Dehalogenase From Xanthobacter
Autotrophicus
Length = 253
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 85 YENLKPDPVLRNLLLSL-PIRKVIFSNADEIHVAKVLRKLGLEDCFDGIVNFES 137
Y L P P L L P+++ I SN + ++ GL D FD +++ ++
Sbjct: 89 YNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDA 142
>pdb|3VWS|A Chain A, Dengue Serotype 3 Rna-dependent Rna Polymerase Bound To
Nitd-107
pdb|4HHJ|A Chain A, Dengue Serotype 3 Rna-dependent Rna Polymerase
Length = 635
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 159 AHHFFQRLFFDDSTRNIECGKSIGLHTVLVGTSRRTKGADYALENIHNIREAFPELW 215
+HHF + + D + C L+G +R ++GA ++L + +A+ ++W
Sbjct: 445 SHHFHELIMKDGRKLVVPCRP----QDELIGRARISQGAGWSLRETACLGKAYAQMW 497
>pdb|2J7U|A Chain A, Dengue Virus Ns5 Rna Dependent Rna Polymerase Domain
pdb|2J7W|A Chain A, Dengue Virus Ns5 Rna Dependent Rna Polymerase Domain
Complexed With 3'dgtp
Length = 635
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 159 AHHFFQRLFFDDSTRNIECGKSIGLHTVLVGTSRRTKGADYALENIHNIREAFPELW 215
+HHF + + D + C L+G +R ++GA ++L + +A+ ++W
Sbjct: 445 SHHFHELIMKDGRKLVVPCRP----QDELIGRARISQGAGWSLRETACLGKAYAQMW 497
>pdb|1W36|B Chain B, Recbcd:dna Complex
pdb|1W36|E Chain E, Recbcd:dna Complex
pdb|3K70|B Chain B, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
pdb|3K70|E Chain E, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
Length = 1180
Score = 27.7 bits (60), Expect = 6.2, Method: Composition-based stats.
Identities = 32/136 (23%), Positives = 63/136 (46%), Gaps = 21/136 (15%)
Query: 47 EFNRVLYKNYGTSMAGLKAVGYDFDNDDYHS-------FVHGRLPYENLKPDPVLRNLLL 99
E L TSM GL A+ + N+D H+ F R + P+LR L+
Sbjct: 607 ERENTLRSALATSMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMPMLRALMS 666
Query: 100 SLPIRKVIFSNA-------DEIHVAKVLRKLGLE-DCFDGIVNFES---LNPTNKTTGQE 148
+ I + + + A D +H++++L++ G + + +V + S L P + + Q+
Sbjct: 667 ARNIAENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEPDSNASSQQ 726
Query: 149 LQLIS---MLRMVAHH 161
++L S ++++V H
Sbjct: 727 MRLESDKHLVQIVTIH 742
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,334,090
Number of Sequences: 62578
Number of extensions: 296763
Number of successful extensions: 771
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 756
Number of HSP's gapped (non-prelim): 15
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
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: 50 (23.9 bits)