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= psy13817
(164 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JVM|A Chain A, Solution Nmr Structure Of Rhodobacter Sphaeroides
Protein Rhos4_26430. Northeast Structural Genomics
Consortium Target Rhr95
Length = 80
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 41 VWCDGGSGPTGHPKVYINLRPEISYI 66
V CDGG G GHP+V++++ E ++
Sbjct: 29 VACDGGEGALGHPRVWLSIPHETGFV 54
Score = 30.4 bits (67), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 146 VWCDGGSGPTGHPKVYINL 164
V CDGG G GHP+V++++
Sbjct: 29 VACDGGEGALGHPRVWLSI 47
>pdb|3D5P|A Chain A, Crystal Structure Of A Putative Glucan Synthesis
Regulator Of Smi1KNR4 FAMILY (BF1740) FROM BACTEROIDES
FRAGILIS NCTC 9343 AT 1.45 A Resolution
pdb|3D5P|B Chain B, Crystal Structure Of A Putative Glucan Synthesis
Regulator Of Smi1KNR4 FAMILY (BF1740) FROM BACTEROIDES
FRAGILIS NCTC 9343 AT 1.45 A Resolution
Length = 144
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 2 FEKDDYRPVRFVDKEKHVNTQFAIDLIAEVPPKPCKERVVWCDGGSGPTGHPKVYI 57
++KD D EK +NT PK K ++W +GG G G +YI
Sbjct: 10 YKKDGASSASIDDVEKLLNTTL---------PKQYKSFLLWSNGGEGKLGDNYIYI 56
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 107 FEKDDYRPVRFVDKEKHVNTQFAIDLIAEVPPKPCKERVVWCDGGSGPTGHPKVYI 162
++KD D EK +NT PK K ++W +GG G G +YI
Sbjct: 10 YKKDGASSASIDDVEKLLNTTL---------PKQYKSFLLWSNGGEGKLGDNYIYI 56
>pdb|2JRR|A Chain A, Solution Nmr Structure Of Q5lls5 From Silicibacter
Pomeroyi. Northeast Structural Genomics Consortium
Target Sir90
Length = 67
Score = 31.2 bits (69), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 37 KERVVWCDGGSGPTGHPKVYINLRPEISYI 66
K RV CDGG G GHP+V++ + + ++
Sbjct: 13 KSRVA-CDGGEGALGHPRVWLQIPEDTGWV 41
Score = 29.6 bits (65), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 142 KERVVWCDGGSGPTGHPKVYINL 164
K RV CDGG G GHP+V++ +
Sbjct: 13 KSRVA-CDGGEGALGHPRVWLQI 34
>pdb|1W7P|D Chain D, The Crystal Structure Of Endosomal Complex Escrt-Ii
(Vps22VPS25VPS36)
Length = 566
Score = 28.1 bits (61), Expect = 2.1, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 55 VYINLRPEISYIMSLLSLLKQTRVNRLIVPLTRTL-AKDVAPFNDIETHTGQKFEKDDYR 113
++ N +++ +MSL + +++ N I T+TL +D + N+ +T R
Sbjct: 342 LFNNALTDLNKLMSLATSIERLYKNSNITMKTKTLNLQDESTVNEPKTR----------R 391
Query: 114 PVRFVDKEKHVNTQFAIDLIA 134
P+ +D+EK +N + +D IA
Sbjct: 392 PLLILDREKFLNKELFLDEIA 412
>pdb|2H9U|A Chain A, Crystal Structure Of The Archaea Specific Dna Binding
Protein
pdb|3U6Y|A Chain A, Crystal Structure Of Alba2-Dna Complex
pdb|3U6Y|C Chain C, Crystal Structure Of Alba2-Dna Complex
Length = 102
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 10/33 (30%), Positives = 23/33 (69%)
Query: 51 GHPKVYINLRPEISYIMSLLSLLKQTRVNRLIV 83
G P+V I +P ++Y++++L+ L + N+++V
Sbjct: 5 GAPEVRIGRKPVMNYVLAILTTLMEQGTNQVVV 37
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 27.7 bits (60), Expect = 3.4, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 9/96 (9%)
Query: 6 DYRPVRFVDKEKHVNTQFAIDLIAEVP-PKPCKERVVWCDGGSGPTGHPKVYINLRPEIS 64
D RP+RF + EKH++ I ++ P P + + PTG I++RP
Sbjct: 379 DNRPLRFEEFEKHMHN---IVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEG 435
Query: 65 YIMSLLSLLKQTRVNR----LIVPLTRTLAKDVAPF 96
I L+ + Q R+ R L+ LT+ +++D+ +
Sbjct: 436 QIDDLIGEI-QARIERNERVLVTTLTKKMSEDLTDY 470
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 27.7 bits (60), Expect = 3.4, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 9/96 (9%)
Query: 6 DYRPVRFVDKEKHVNTQFAIDLIAEVP-PKPCKERVVWCDGGSGPTGHPKVYINLRPEIS 64
D RP+RF + EKH++ I ++ P P + + PTG I++RP
Sbjct: 373 DNRPLRFEEFEKHMHN---IVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEG 429
Query: 65 YIMSLLSLLKQTRVNR----LIVPLTRTLAKDVAPF 96
I L+ + Q R+ R L+ LT+ +++D+ +
Sbjct: 430 QIDDLIGEI-QARIERNERVLVTTLTKKMSEDLTDY 464
>pdb|2BGW|A Chain A, Xpf From Aeropyrum Pernix, Complex With Dna
pdb|2BGW|B Chain B, Xpf From Aeropyrum Pernix, Complex With Dna
Length = 219
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 4/96 (4%)
Query: 49 PTGHPKVYINLRPEISYIMSLLSLLKQTRVNRLIVPLTRTLAKDVAPFNDIETHTGQKFE 108
P G P+VY+++R E S + S+L L + + + P+ L D +E T F
Sbjct: 5 PGGRPRVYVDVREERSPVPSILESLGVQVIPKQL-PMGDYLVSDSII---VERKTSSDFA 60
Query: 109 KDDYRPVRFVDKEKHVNTQFAIDLIAEVPPKPCKER 144
K + F + + +I E PP P + R
Sbjct: 61 KSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYR 96
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 0.140 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,526,249
Number of Sequences: 62578
Number of extensions: 221045
Number of successful extensions: 368
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 358
Number of HSP's gapped (non-prelim): 18
length of query: 164
length of database: 14,973,337
effective HSP length: 91
effective length of query: 73
effective length of database: 9,278,739
effective search space: 677347947
effective search space used: 677347947
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: 47 (22.7 bits)