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= 038243
(680 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 354 YRGVTRHHQHGRWQARIGRVAGN-KDLYLGTFSTQXXXXXXYDIAAIKFRGLNAVTNFDM 412
YRGV R G++ A I A N ++LGTF T YD AA + RG A+ NF +
Sbjct: 3 YRGV-RQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 61
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 255 YRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQ---GGYDKEEKAARAYDLAALKYWGTT 311
YRGV + W G++ A + D + + G + G ++ E AA AYD AA + G+
Sbjct: 3 YRGVRQRPW-GKFAAEIRDPA-------KNGARVWLGTFETAEDAALAYDRAAFRMRGSR 54
Query: 312 TTTNFPI 318
NFP+
Sbjct: 55 ALLNFPL 61
>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 = 36.6 bits (83), Expect = 0.047, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 354 YRGVTRHHQHGRWQARIGRVAGN-KDLYLGTFSTQXXXXXXYDIAAIKFRGLNAVTNFDM 412
YRGV R G++ A I A N ++LGTF T YD AA + RG A+ NF +
Sbjct: 6 YRGV-RQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 64
Score = 33.5 bits (75), Expect = 0.36, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 255 YRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQ---GGYDKEEKAARAYDLAALKYWGTT 311
YRGV + W G++ A + D + + G + G ++ E AA AYD AA + G+
Sbjct: 6 YRGVRQRPW-GKFAAEIRDPA-------KNGARVWLGTFETAEDAALAYDRAAFRMRGSR 57
Query: 312 TTTNFPI 318
NFP+
Sbjct: 58 ALLNFPL 64
>pdb|3A5C|A Chain A, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5C|B Chain B, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5C|C Chain C, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5C|I Chain I, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5C|J Chain J, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5C|K Chain K, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5D|A Chain A, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5D|B Chain B, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5D|C Chain C, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5D|I Chain I, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5D|J Chain J, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3A5D|K Chain K, Inter-Subunit Interaction And Quaternary Rearrangement
Defined By The Central Stalk Of Prokaryotic V1-Atpase
pdb|3J0J|A Chain A, Fitted Atomic Models Of Thermus Thermophilus V-Atpase
Subunits Into Cryo-Em Map
pdb|3J0J|B Chain B, Fitted Atomic Models Of Thermus Thermophilus V-Atpase
Subunits Into Cryo-Em Map
pdb|3J0J|C Chain C, Fitted Atomic Models Of Thermus Thermophilus V-Atpase
Subunits Into Cryo-Em Map
Length = 578
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 434 RLKDAEQAAEMTIDRPTVVADDENMSSQLTADHGWP 469
R+K+ + A E T++ P VV +D ++L H WP
Sbjct: 156 RVKEVKPAGEYTVEEPVVVLED---GTELKMYHTWP 188
>pdb|3GQB|A Chain A, Crystal Structure Of The A3b3 Complex From V-atpase
pdb|3GQB|C Chain C, Crystal Structure Of The A3b3 Complex From V-atpase
Length = 578
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 434 RLKDAEQAAEMTIDRPTVVADDENMSSQLTADHGWP 469
R+K+ + A E T++ P VV +D ++L H WP
Sbjct: 156 RVKEVKPAGEYTVEEPVVVLED---GTELKMYHTWP 188
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 29.6 bits (65), Expect = 5.3, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 314 TNFPISNYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRV 373
+N P+S E+E+E M Q + R SSG SRG G R + +A IG
Sbjct: 31 SNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV----GFARMESTEKCEAVIGHF 86
Query: 374 AG 375
G
Sbjct: 87 NG 88
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
0.317 0.130 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,944,151
Number of Sequences: 62578
Number of extensions: 547350
Number of successful extensions: 1054
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1048
Number of HSP's gapped (non-prelim): 10
length of query: 680
length of database: 14,973,337
effective HSP length: 105
effective length of query: 575
effective length of database: 8,402,647
effective search space: 4831522025
effective search space used: 4831522025
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: 55 (25.8 bits)