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= 023865
(276 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3QKY|A Chain A, Crystal Structure Of Rhodothermus Marinus Bamd
Length = 261
Score = 35.0 bits (79), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 164 RRATAQLMFELGQKAYGKGMYGRAIEFLEGALTIIPRPTFFGGEIQIWLAMAYEANNRH 222
R ++ Q FE + Y +G Y RAIE+ + T R + + Q +LA AY N +
Sbjct: 11 RHSSPQEAFERAMEFYNQGKYDRAIEYFKAVFT-YGRTHEWAADAQFYLARAYYQNKEY 68
>pdb|4H62|Q Chain Q, Structure Of The Saccharomyces Cerevisiae Mediator
Subcomplex Med17cMED11CMED22C
Length = 312
Score = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 30 ALDVLLNLPKRDLHLNYSALANK----SLDSEGESW-NHRVVTRGKVNSKVNAVDFDAGS 84
A D LLN+P+R+L +N +K SL E ++ N + + ++ NAV FD
Sbjct: 230 AFDKLLNIPRRELKINLPLTEHKSPNLSLXLESPNYCNALIHIKFSAGTEANAVSFDTTF 289
Query: 85 SD 86
SD
Sbjct: 290 SD 291
>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Trigonal Crystal Form)
pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Orthorombic Crystal Form)
Length = 136
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 167 TAQLMFELGQKAYGKGMYGRAIEFLEGALTIIPR 200
+A+ + LG Y +G Y AIE+ + AL + PR
Sbjct: 34 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 67
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 167 TAQLMFELGQKAYGKGMYGRAIEFLEGALTIIPR 200
+A+ + LG Y +G Y AIE+ + AL + PR
Sbjct: 68 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 101
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 167 TAQLMFELGQKAYGKGMYGRAIEFLEGALTIIPR 200
+A+ + LG Y +G Y AIE+ + AL + PR
Sbjct: 102 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 135
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 168 AQLMFELGQKAYGKGMYGRAIEFLEGALTIIPR 200
A+ + LG Y +G Y AIE+ + AL + PR
Sbjct: 1 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 33
>pdb|2AVP|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
Length = 70
Score = 30.8 bits (68), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 166 ATAQLMFELGQKAYGKGMYGRAIEFLEGALTIIPRPTFFGGEIQIW--LAMAYEANNRHA 223
+A+ + LG Y +G Y AIE+ + AL + PR + W L AY +
Sbjct: 1 GSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSA------EAWYNLGNAYYKQGDYD 54
Query: 224 DCIALYKQ 231
+ I Y++
Sbjct: 55 EAIEYYQK 62
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 167 TAQLMFELGQKAYGKGMYGRAIEFLEGALTIIPR 200
+A+ + LG Y +G Y AIE+ + AL + PR
Sbjct: 36 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 69
>pdb|4GWP|B Chain B, Structure Of The Mediator Head Module From S. Cerevisiae
pdb|4GWQ|B Chain B, Structure Of The Mediator Head Module From S. Cerevisiae
In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
Polymerase Ii Rpb1 Subunit
Length = 687
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 30 ALDVLLNLPKRDLHLNYSALANK----SLDSEGESW-NHRVVTRGKVNSKVNAVDFDAGS 84
A D LLN+P+R+L +N +K SL E ++ N + + ++ NAV FD
Sbjct: 605 AFDKLLNIPRRELKINLPLTEHKSPNLSLMLESPNYCNALIHIKFSAGTEANAVSFDTTF 664
Query: 85 SD 86
SD
Sbjct: 665 SD 666
>pdb|2VED|A Chain A, Crystal Structure Of The Chimerical Mutant Capabk55m
Protein
pdb|2VED|B Chain B, Crystal Structure Of The Chimerical Mutant Capabk55m
Protein
Length = 271
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 1 MAVVVGNLALLLDVASPRTLITDRKSRPLALDVLLNLPKRD----LHLNYSALANKSLDS 56
M+ + NLA+ A +TLI D R + NLP + L LN+S + + +
Sbjct: 96 MSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIIST 155
Query: 57 EGESWNHRVVTRGKV 71
E E + V+T G +
Sbjct: 156 EIEDLD--VLTSGPI 168
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 0.133 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,955,582
Number of Sequences: 62578
Number of extensions: 199593
Number of successful extensions: 364
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 357
Number of HSP's gapped (non-prelim): 11
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)