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= psy16510
(147 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3S5Q|A Chain A, Crystal Structure Of A Hypothetical Glycosyl Hydrolase
(Bdi_2473) From Parabacteroides Distasonis Atcc 8503 At
1.85 A Resolution
Length = 214
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 66 ANEQGYLKNPGQKDLEAQTAQGQFTYTAPDGTPITVQWFADETG--FHASGAHLPTPPPI 123
ANEQ +K PG+ + TA+GQ +G I AD T + G +P PI
Sbjct: 123 ANEQLVVKKPGEWNRXIITAKGQQIDIELNGKHIVSANLADWTSGTTNPDGTEIPEWLPI 182
Query: 124 PEA 126
P A
Sbjct: 183 PYA 185
>pdb|3M4A|A Chain A, Crystal Structure Of A Bacterial Topoisomerase Ib In
Complex With Dna Reveals A Secondary Dna Binding Site
Length = 346
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 26/62 (41%), Gaps = 17/62 (27%)
Query: 88 QFTYTAPDGTPITVQWFADETGFHASGAHLPTPPPIPEAILKSLQQVQVSPPGPNR---F 144
+F Y PDGTP T D G A A L PP + Q V VSP N F
Sbjct: 22 KFRYVHPDGTPYT-----DADGL-ARIARLAVPP--------AYQDVYVSPDAENELQAF 67
Query: 145 GR 146
GR
Sbjct: 68 GR 69
>pdb|2F4Q|A Chain A, Crystal Structure Of Deinococcus Radiodurans Topoisomerase
Ib
Length = 346
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 26/62 (41%), Gaps = 17/62 (27%)
Query: 88 QFTYTAPDGTPITVQWFADETGFHASGAHLPTPPPIPEAILKSLQQVQVSPPGPNR---F 144
+F Y PDGTP T D G A A L PP + Q V VSP N F
Sbjct: 22 KFRYVHPDGTPYT-----DADGL-ARIARLAVPP--------AYQDVYVSPDAENELQAF 67
Query: 145 GR 146
GR
Sbjct: 68 GR 69
>pdb|4EW7|A Chain A, The Crystal Structure Of Conjugative Transfer Pas_like
Domain From Salmonella Enterica Subsp. Enterica Serovar
Typhimurium
Length = 127
Score = 27.3 bits (59), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 21 AVVSAQRGPPQYAPGQFIPIISYQNEPNQGDGSYRYSYET 60
V Q YA G FI + S +++P GD RY E
Sbjct: 33 VCVRNQSRKIIYANGAFIELFSKEDQPLSGDSYNRYGVEV 72
>pdb|4F53|A Chain A, Crystal Structure Of A Susd Homolog (Bacova_04803) From
Bacteroides Ovatus Atcc 8483 At 2.25 A Resolution
pdb|4F53|B Chain B, Crystal Structure Of A Susd Homolog (Bacova_04803) From
Bacteroides Ovatus Atcc 8483 At 2.25 A Resolution
Length = 520
Score = 26.6 bits (57), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 7/54 (12%)
Query: 55 RYSYETGNGIAANEQGYLKNPGQ----KD-LEAQTAQGQFTYTAPDGTPITVQW 103
R S+E NGI + + YL + G+ KD L+ Q+AQ + Y+ T +TV W
Sbjct: 367 RLSFEE-NGITSGVENYLASTGKVEAYKDPLKGQSAQ-TYDYSGAINTNVTVAW 418
>pdb|2CW5|A Chain A, Crystal Structure Of A Conserved Hypothetical Protein From
Thermus Thermophilus Hb8
pdb|2CW5|B Chain B, Crystal Structure Of A Conserved Hypothetical Protein From
Thermus Thermophilus Hb8
pdb|2CW5|C Chain C, Crystal Structure Of A Conserved Hypothetical Protein From
Thermus Thermophilus Hb8
Length = 255
Score = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 81 EAQTAQGQFTYTAPDGTPITVQWFAD 106
A A G++TY PD T+ W D
Sbjct: 78 RAVAALGRWTYVGPDNGLFTLAWLLD 103
>pdb|2ZYG|A Chain A, Apo-Form Of Dimeric 6-Phosphogluconate Dehydrogenase
pdb|2ZYG|B Chain B, Apo-Form Of Dimeric 6-Phosphogluconate Dehydrogenase
Length = 480
Score = 26.2 bits (56), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 25/63 (39%), Gaps = 7/63 (11%)
Query: 61 GNGIAANEQGYLKNP-----GQKDLEAQTA--QGQFTYTAPDGTPITVQWFADETGFHAS 113
G G++ E+G LK P GQK+ A Q A DG P AD G +
Sbjct: 136 GTGVSGGEEGTLKGPSIMPGGQKEAYELVAPILKQIAAVAEDGEPCVTYIGADGAGHYVK 195
Query: 114 GAH 116
H
Sbjct: 196 MVH 198
>pdb|1V6F|A Chain A, Solution Structure Of Glia Maturation Factor-Beta From Mus
Musculus
Length = 151
Score = 25.8 bits (55), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 22/109 (20%), Positives = 48/109 (44%), Gaps = 2/109 (1%)
Query: 1 MMKIEKDIGALAISFVALFIAVVSAQRGPPQYAPGQFIPIISYQNEPNQGDGSYRYSYET 60
+MKI+KD + + ++ + P+ P +FI + SY+ + + G SY +
Sbjct: 39 IMKIDKDERLVVLDEELEGVSPDELKDELPERQP-RFI-VYSYKYQHDDGRVSYPLCFIF 96
Query: 61 GNGIAANEQGYLKNPGQKDLEAQTAQGQFTYTAPDGTPITVQWFADETG 109
+ + + + G K+ QTA+ + + +T +W ++ G
Sbjct: 97 SSPVGCKPEQQMMYAGSKNKLVQTAELTKVFEIRNTEDLTEEWLREKLG 145
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
0.315 0.135 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,198,341
Number of Sequences: 62578
Number of extensions: 238506
Number of successful extensions: 403
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 401
Number of HSP's gapped (non-prelim): 16
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 bits)