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= psy7344
(240 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3B0V|C Chain C, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
pdb|3B0V|D Chain D, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
Length = 363
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 106 LGFKTRSHMCGHSLMFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQ 164
L F+ H +L G+D K+L EAA++ E D I++N+GCP A+ G YGA L
Sbjct: 72 LAFRPEEHPI--ALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLL 129
Query: 165 DDWPLLTNLVYS 176
D + ++ +
Sbjct: 130 LDLARVREILKA 141
Score = 30.4 bits (67), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 16 DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTELV 49
D I++N+GCP A+ G YGA L D + E++
Sbjct: 106 DEINLNLGCPSEKAQEGGYGACLLLDLARVREIL 139
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 74 DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTEL 106
D I++N+GCP A+ G YGA L D + E+
Sbjct: 106 DEINLNLGCPSEKAQEGGYGACLLLDLARVREI 138
Score = 27.3 bits (59), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 190 DGNDINIGCPQMVAKRGHYGAYLQDDWPLLTELGK 224
D ++N+GCP A+ G YGA L D + E+ K
Sbjct: 106 DEINLNLGCPSEKAQEGGYGACLLLDLARVREILK 140
>pdb|3B0P|A Chain A, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0P|B Chain B, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0U|X Chain X, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
pdb|3B0U|Y Chain Y, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
Length = 350
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 106 LGFKTRSHMCGHSLMFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQ 164
L F+ H +L G+D K+L EAA++ E D I++N+GCP A+ G YGA L
Sbjct: 51 LAFRPEEHPI--ALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLL 108
Query: 165 DDWPLLTNLVYS 176
D + ++ +
Sbjct: 109 LDLARVREILKA 120
Score = 30.4 bits (67), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 16 DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTELV 49
D I++N+GCP A+ G YGA L D + E++
Sbjct: 85 DEINLNLGCPSEKAQEGGYGACLLLDLARVREIL 118
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 74 DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTEL 106
D I++N+GCP A+ G YGA L D + E+
Sbjct: 85 DEINLNLGCPSEKAQEGGYGACLLLDLARVREI 117
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 190 DGNDINIGCPQMVAKRGHYGAYLQDDWPLLTELGK 224
D ++N+GCP A+ G YGA L D + E+ K
Sbjct: 85 DEINLNLGCPSEKAQEGGYGACLLLDLARVREILK 119
>pdb|1VHN|A Chain A, Crystal Structure Of A Putative Flavin Oxidoreductase With
Flavin
Length = 318
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 113 HMCGHSLMFCGNDSKNLTEAAKLAEPHCDGIDINIGCP-QMVAKRGHYGAYLQD 165
H ++ G++ L+EAA++ ID+N GCP + V K G GA L+D
Sbjct: 57 HERNVAVQIFGSEPNELSEAARILSEKYKWIDLNAGCPVRKVVKEGAGGALLKD 110
>pdb|5CSM|A Chain A, Yeast Chorismate Mutase, T226s Mutant, Complex With Trp
Length = 256
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 14/59 (23%)
Query: 190 DGNDIN---------IGCPQMVAKRGHYGAYL-----QDDWPLLTELGKMAMLVGILDN 234
DG+D N I C Q +++R H+G ++ Q D PL T+L K + GI+ N
Sbjct: 133 DGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKN 191
>pdb|3CSM|A Chain A, Structure Of Yeast Chorismate Mutase With Bound Trp And An
Endooxabicyclic Inhibitor
pdb|3CSM|B Chain B, Structure Of Yeast Chorismate Mutase With Bound Trp And An
Endooxabicyclic Inhibitor
Length = 256
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 14/59 (23%)
Query: 190 DGNDIN---------IGCPQMVAKRGHYGAYL-----QDDWPLLTELGKMAMLVGILDN 234
DG+D N I C Q +++R H+G ++ Q D PL T+L K + GI+ N
Sbjct: 133 DGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKN 191
>pdb|4CSM|A Chain A, Yeast Chorismate Mutase + Tyr + Endooxabicyclic Inhibitor
pdb|4CSM|B Chain B, Yeast Chorismate Mutase + Tyr + Endooxabicyclic Inhibitor
pdb|2CSM|A Chain A, Tyr-Bound T-State Of Yeast Chorismate Mutase
Length = 256
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 14/59 (23%)
Query: 190 DGNDIN---------IGCPQMVAKRGHYGAYL-----QDDWPLLTELGKMAMLVGILDN 234
DG+D N I C Q +++R H+G ++ Q D PL T+L K + GI+ N
Sbjct: 133 DGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKN 191
>pdb|1CSM|A Chain A, The Crystal Structure Of Allosteric Chorismate Mutase At
2.2 Angstroms Resolution
pdb|1CSM|B Chain B, The Crystal Structure Of Allosteric Chorismate Mutase At
2.2 Angstroms Resolution
Length = 256
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 14/59 (23%)
Query: 190 DGNDIN---------IGCPQMVAKRGHYGAYL-----QDDWPLLTELGKMAMLVGILDN 234
DG+D N I C Q +++R H+G ++ Q D PL T+L K + GI+ N
Sbjct: 133 DGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKN 191
>pdb|3S6O|A Chain A, Crystal Structure Of A Polysaccharide Deacetylase Family
Protein From Burkholderia Pseudomallei
pdb|3S6O|B Chain B, Crystal Structure Of A Polysaccharide Deacetylase Family
Protein From Burkholderia Pseudomallei
pdb|3S6O|C Chain C, Crystal Structure Of A Polysaccharide Deacetylase Family
Protein From Burkholderia Pseudomallei
pdb|3S6O|D Chain D, Crystal Structure Of A Polysaccharide Deacetylase Family
Protein From Burkholderia Pseudomallei
Length = 321
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 158 HYGAYLQDDWPLLTNLVYSPNM-VHFVIAEPHCDGNDINIGCPQMVAKRGHYGAYLQDDW 216
HYG DD P ++ S V +I D ND+ PQ H+ YL+D +
Sbjct: 193 HYG----DDLPFWMDVEVSGGASVPQLIVPYTLDANDMRFATPQGFNTADHFFHYLRDAF 248
Query: 217 PLLTELGKMA 226
+L E G A
Sbjct: 249 DVLYEEGDEA 258
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
0.322 0.142 0.480
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,192,068
Number of Sequences: 62578
Number of extensions: 345858
Number of successful extensions: 556
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 543
Number of HSP's gapped (non-prelim): 16
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
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: 50 (23.9 bits)