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= 042427
(229 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3G26|A Chain A, Crystal Structure Of The C-Terminal Domain Of The Rous
Sarcoma Virus Capsid Protein: Mutant A184c
Length = 77
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 171 PWVVVNNQPLQEDFMNFANHVCKAYKGTGLPEACRS 206
PW + P E F++FAN + KA +G+ LP +CR+
Sbjct: 3 PWADIMQGP-SESFVDFANRLIKAVEGSDLPPSCRA 37
>pdb|1D1D|A Chain A, Nmr Solution Structure Of The Capsid Protein From Rous
Sarcoma Virus
Length = 262
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 159 ETAQLKPPHRFVPWVVVNNQPLQEDFMNFANHVCKAYKGTGLPEACRS 206
E A+L P PW + P E F++FAN + KA +G+ LP + R+
Sbjct: 164 EVARLAEPAG--PWADITQGP-SESFVDFANRLIKAVEGSDLPPSARA 208
>pdb|2X8Q|A Chain A, Cryo-Em 3d Model Of The Icosahedral Particle Composed Of
Rous Sarcoma Virus Capsid Protein Pentamers
pdb|3TIR|A Chain A, Pseudo-Atomic Model Of The Rous Sarcoma Virus Capsid
Hexamer
Length = 226
Score = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 159 ETAQLKPPHRFVPWVVVNNQPLQEDFMNFANHVCKAYKGTGLPEACRS 206
E A+L P PW + P E F++FAN + KA +G+ LP + R+
Sbjct: 142 EVARLAEPAG--PWADIMQGP-SESFVDFANRLIKAVEGSDLPPSARA 186
>pdb|3G0V|A Chain A, Crystal Structure Of The C-Terminal Domain From The Rous
Sarcoma Virus Capsid Protein: Mutant D179a
Length = 77
Score = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 171 PWVVVNNQPLQEDFMNFANHVCKAYKGTGLPEACRS 206
PW + P E F++FAN + KA +G+ LP + R+
Sbjct: 3 PWADIMQGP-SESFVDFANRLIKAVEGSALPPSARA 37
>pdb|3G1G|A Chain A, Crystal Structure Of The C-Terminal Domain From The Rous
Sarcoma Virus Capsid Protein: High Ph
pdb|3G1G|B Chain B, Crystal Structure Of The C-Terminal Domain From The Rous
Sarcoma Virus Capsid Protein: High Ph
Length = 87
Score = 34.3 bits (77), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 171 PWVVVNNQPLQEDFMNFANHVCKAYKGTGLPEACRS 206
PW + P E F++FAN + KA +G+ LP + R+
Sbjct: 2 PWADIMQGP-SESFVDFANRLIKAVEGSDLPPSARA 36
>pdb|3G1I|A Chain A, Crystal Structure Of The C-Terminal Domain Of The Rous
Sarcoma Virus Capsid Protein: Intermediate Ph
pdb|3G1I|B Chain B, Crystal Structure Of The C-Terminal Domain Of The Rous
Sarcoma Virus Capsid Protein: Intermediate Ph
pdb|3G21|A Chain A, Crystal Structure Of The C-Terminal Domain Of The Rous
Sarcoma Virus Capsid Protein: Low Ph
Length = 77
Score = 33.9 bits (76), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 171 PWVVVNNQPLQEDFMNFANHVCKAYKGTGLPEACRS 206
PW + P E F++FAN + KA +G+ LP + R+
Sbjct: 3 PWADIMQGP-SESFVDFANRLIKAVEGSDLPPSARA 37
>pdb|3G28|A Chain A, Crystal Structure Of The C-Terminal Domain Of The Rous
Sarcoma Virus Capsid Protein: Mutant D179n, Low Ph
pdb|3G29|A Chain A, Crystal Structure Of The C-Terminal Domain Of The Rous
Sarcoma Virus Capsid Protein: D179n Mutant, Neutral Ph
pdb|3G29|B Chain B, Crystal Structure Of The C-Terminal Domain Of The Rous
Sarcoma Virus Capsid Protein: D179n Mutant, Neutral Ph
Length = 77
Score = 33.9 bits (76), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 171 PWVVVNNQPLQEDFMNFANHVCKAYKGTGLPEACRS 206
PW + P E F++FAN + KA +G+ LP + R+
Sbjct: 3 PWADIMQGP-SESFVDFANRLIKAVEGSNLPPSARA 37
>pdb|1EOQ|A Chain A, Rous Sarcoma Virus Capsid Protein: C-Terminal Domain
Length = 96
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 182 EDFMNFANHVCKAYKGTGLPEACRS 206
E F++FAN + KA +G+ LP + R+
Sbjct: 9 ESFVDFANRLIKAVEGSDLPPSARA 33
>pdb|1JRK|A Chain A, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1JRK|B Chain B, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1JRK|C Chain C, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1JRK|D Chain D, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1K26|A Chain A, Structure Of A Nudix Protein From Pyrobaculum Aerophilum
Solved By The Single Wavelength Anomolous Scattering
Method
pdb|1K26|B Chain B, Structure Of A Nudix Protein From Pyrobaculum Aerophilum
Solved By The Single Wavelength Anomolous Scattering
Method
pdb|1K2E|A Chain A, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum
pdb|1K2E|B Chain B, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum
Length = 156
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 102 YPDVVQ-HFSFIHCVERLALEKRQAEWINCFELTKLGRVP 140
YP+ HF I+ V+R+ + + EWI+ E+ ++ P
Sbjct: 84 YPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFP 123
>pdb|3FZV|A Chain A, Crystal Structure Of Pa01 Protein, Putative Lysr Family
Transcriptional Regulator From Pseudomonas Aeruginosa
pdb|3FZV|B Chain B, Crystal Structure Of Pa01 Protein, Putative Lysr Family
Transcriptional Regulator From Pseudomonas Aeruginosa
pdb|3FZV|C Chain C, Crystal Structure Of Pa01 Protein, Putative Lysr Family
Transcriptional Regulator From Pseudomonas Aeruginosa
pdb|3FZV|D Chain D, Crystal Structure Of Pa01 Protein, Putative Lysr Family
Transcriptional Regulator From Pseudomonas Aeruginosa
Length = 306
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 125 AEWINCFELTKLGRVPIDCYRNGLGKLLEQKY 156
A W+ +LTK R+ +D R LGKL E+++
Sbjct: 275 AAWLKRAQLTKPARLFVDYCREQLGKLAERRH 306
>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS
Bound To Origin Dna (From S. Solfataricus)
Length = 386
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 6 LLTFFFPASLLLLSISPFGSSENV--TVSVYYETLCPYCADFIVNHLVKLFQKGLNSIVN 63
+LT F + L+L+++ S ENV T YET C V + Q+ ++ I+N
Sbjct: 281 ILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKLGVEAVT---QRRVSDIIN 337
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
0.323 0.138 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,190,759
Number of Sequences: 62578
Number of extensions: 287666
Number of successful extensions: 510
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 500
Number of HSP's gapped (non-prelim): 11
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)