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= 039060
(1040 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WEO|A Chain A, Solution Structure Of Ring-Finger In The Catalytic
Subunit (Irx3) Of Cellulose Synthase
Length = 93
Score = 142 bits (358), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 63/70 (90%), Positives = 66/70 (94%)
Query: 26 PKPLKNLDAQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQVCPQCKTR 85
PKPLKNLD Q CEICGD+IGLTV+GDLFVACNECGFP CRPCYEYERREGTQ CPQCKTR
Sbjct: 8 PKPLKNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTR 67
Query: 86 YKRLKGSPRV 95
YKRL+GSPRV
Sbjct: 68 YKRLRGSPRV 77
>pdb|4HG6|A Chain A, Structure Of A Cellulose Synthase - Cellulose
Translocation Intermediate
Length = 802
Score = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 31/109 (28%), Positives = 51/109 (46%), Gaps = 7/109 (6%)
Query: 730 GWIYGSITEDILTGFKMHCRGWRSIYCMPKRAAFKGSAPINLSDRLNQVLRWALGSVEIF 789
G+ +ITED T ++H RGW+S+Y RA G P + + Q RWA G +++
Sbjct: 334 GFAGETITEDAETALEIHSRGWKSLYI--DRAMIAGLQPETFASFIQQRGRWATGMMQML 391
Query: 790 FSRHSPVWYGYKGGNLRFLERFAYVNTTIYPFTSIPLLAYCVLPAICLL 838
++ G L +R Y+N+ + F + + + V P I L
Sbjct: 392 LLKNPLFRRG-----LGIAQRLCYLNSMSFWFFPLVRMMFLVAPLIYLF 435
Score = 47.4 bits (111), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 43/129 (33%), Positives = 59/129 (45%), Gaps = 21/129 (16%)
Query: 499 LVYVSREKRPGFQHHKKAGAMNA-LVRVSGVLTNAPFMLNLDCDHYVNNSKAVRESMCFL 557
+VY +RE+ H KAG M+A L R+ G L ++ D DH + R F+
Sbjct: 214 VVYSTRER----NEHAKAGNMSAALERLKGEL-----VVVFDADHVPSRDFLARTVGYFV 264
Query: 558 MDPQTGRKVCYVQFPQRF---DGIDRH----DRYANRNTVFFDINMRGLDGIQGPVYVGT 610
DP + VQ P F D I R+ DR N +F+ RGLD G + G+
Sbjct: 265 EDPD----LFLVQTPHFFINPDPIQRNLALGDRCPPENEMFYGKIHRGLDRWGGAFFCGS 320
Query: 611 GCVFRRQAL 619
V RR+AL
Sbjct: 321 AAVLRRRAL 329
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 32.0 bits (71), Expect = 2.1, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 26/73 (35%), Gaps = 2/73 (2%)
Query: 22 NHEEPKPLKNLDAQV-CEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQVCP 80
NH+ P+ V C IC D V + ECG C C + + CP
Sbjct: 59 NHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLR-DSLKNANTCP 117
Query: 81 QCKTRYKRLKGSP 93
C+ + + P
Sbjct: 118 TCRKKINHKRYHP 130
Score = 30.8 bits (68), Expect = 4.2, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 37 CEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQVCPQCKTRYKRLKGSP 93
C IC D V + ECG C C + + CP C+ + + P
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLR-DSLKNANTCPTCRKKINHKRYHP 65
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 30.8 bits (68), Expect = 4.2, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 37 CEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQVCPQCKTRYKRLKGSP 93
C IC D V + ECG C C + + CP C+ + + P
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLR-DSLKNANTCPTCRKKINHKRYHP 61
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 30.8 bits (68), Expect = 4.6, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 37 CEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQVCPQCKTRYKRLKGSP 93
C IC D V + ECG C C + + CP C+ + + P
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLR-DSLKNANTCPTCRKKINHKRYHP 68
>pdb|2BMO|B Chain B, The Crystal Structure Of Nitrobenzene Dioxygenase
pdb|2BMQ|B Chain B, The Crystal Structure Of Nitrobenzene Dioxygenase In
Complex With Nitrobenzene
pdb|2BMR|B Chain B, The Crystal Structure Of Nitrobenzene Dioxygenase In
Complex With 3-Nitrotoluene
Length = 194
Score = 30.0 bits (66), Expect = 6.3, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 761 AAFKGSAPINLSDRLNQVLRWAL--GSVEIFFSRHSPVWYGYKGGNLRFLERF 811
AA SAP L R N +L A V++F++ W +GG ++ +ERF
Sbjct: 125 AAKDKSAPEILHVRSNLILHRARRENQVDVFYATREDKWKRIEGGGIKLVERF 177
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 30.0 bits (66), Expect = 6.3, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 37 CEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQVCPQCKTR 85
C IC D V + ECG C C + + CP C+ +
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLR-DSLKNANTCPTCRKK 65
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 0.140 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,046,012
Number of Sequences: 62578
Number of extensions: 1355327
Number of successful extensions: 2454
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2448
Number of HSP's gapped (non-prelim): 11
length of query: 1040
length of database: 14,973,337
effective HSP length: 109
effective length of query: 931
effective length of database: 8,152,335
effective search space: 7589823885
effective search space used: 7589823885
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: 56 (26.2 bits)