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= 045327
(162 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
Minimized Mean Structure
pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
46 Structures
Length = 70
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/65 (46%), Positives = 44/65 (67%), Gaps = 3/65 (4%)
Query: 22 AHQRKYKGIRRRKWGKWVSEIRVPGSQ-ERLWLGSYATPEAAAMAHDVAFYCLRRPRSLD 80
A + Y+G+R+R WGK+ +EIR P R+WLG++ T E AA+A+D A + +R R+L
Sbjct: 1 AKGKHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRAL- 59
Query: 81 GLNFP 85
LNFP
Sbjct: 60 -LNFP 63
>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
Structure
Length = 63
Score = 57.8 bits (138), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 42/60 (70%), Gaps = 3/60 (5%)
Query: 27 YKGIRRRKWGKWVSEIRVPGSQ-ERLWLGSYATPEAAAMAHDVAFYCLRRPRSLDGLNFP 85
Y+G+R+R WGK+ +EIR P R+WLG++ T E AA+A+D A + +R R+L LNFP
Sbjct: 3 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRAL--LNFP 60
>pdb|3H7O|A Chain A, Crystal Structure Of Scabies Mite Inactivated Protease
Paralogue S-I1 (Smipp-S-I1)
pdb|3H7O|B Chain B, Crystal Structure Of Scabies Mite Inactivated Protease
Paralogue S-I1 (Smipp-S-I1)
Length = 228
Score = 33.9 bits (76), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 46/100 (46%), Gaps = 14/100 (14%)
Query: 63 AMAHDVAFYCLRRPRSLDGLNFPSMLPASVVHAELSPKSVQKAASD---AGMGVDAQMVL 119
M +D+A L RP LDGL PA + E PK+ SD +G G D Q +
Sbjct: 85 TMENDIAILELSRPLKLDGLK---SKPAKLPDIEFRPKT----GSDVLVSGYG-DGQTMD 136
Query: 120 NKDKTDEXXXXXXIVERRKCLMRSSFGNMITSLKIVGHRK 159
KD D +V+ +C R+ +G + SL++ +K
Sbjct: 137 PKDH-DLKSAQLTVVDLDEC--RTKYGPIFLSLQVFCAQK 173
>pdb|4EVS|A Chain A, Crystal Structure Of Abc Transporter From R. Palustris -
Solute Binding Protein (Rpa0985) In Complex With
4-Hydroxybenzoate
Length = 371
Score = 30.4 bits (67), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 84 FPSMLPASVVHAELSPKSVQKAASDAGMGVDAQMVLNKDKTDEXXXXXXIVERRKCLMRS 143
F + +PA+ V + K V A SD G G+DA+ KT E + R L +
Sbjct: 124 FQNTVPAAKVAKQKGAKKVAIAVSDYGPGIDAETAFK--KTFEAEGGSVVEAVRXPLATT 181
Query: 144 SFGNMITSLKIVG 156
FG + +K G
Sbjct: 182 DFGPIXQRIKDSG 194
>pdb|4F06|A Chain A, Crystal Structure Of Solute Binding Protein Of Abc
Transporter From Rhodopseudomonas Palustris Haa2
Rpb_2270 In Complex With P- Hydroxybenzoic Acid
Length = 371
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 84 FPSMLPASVVHAELSPKSVQKAASDAGMGVDAQMVLNKDKTDEXXXXXXIVERRKCLMRS 143
F + +PA+ V + V A SD G G+DA+ KT E + R L +
Sbjct: 124 FQNTVPAAKVAKQKGATKVAIAVSDYGPGIDAETAFK--KTFEAEGGKVVEAVRXPLSTT 181
Query: 144 SFGNMITSLK 153
FG + +K
Sbjct: 182 DFGPIXQRIK 191
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
0.318 0.131 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,409,892
Number of Sequences: 62578
Number of extensions: 152492
Number of successful extensions: 243
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 237
Number of HSP's gapped (non-prelim): 5
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
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)