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= 013364
(444 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FH5|A Chain A, The Structure Of The Mammalian Srp Receptor
pdb|2GO5|1 Chain 1, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
Length = 185
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 40/99 (40%), Positives = 62/99 (62%), Gaps = 5/99 (5%)
Query: 1 MLEQLLIFTRGGLILWTCKELGNALKGSPIDTLIRSCLLEERSGLASFNYDSAGAAYTLK 60
M++ IF++GGL+LW + + ++ G P++ LIRS LL+ER G SF ++ A TLK
Sbjct: 10 MVDFFTIFSKGGLVLWCFQGVSDSCTG-PVNALIRSVLLQERGGNNSFTHE----ALTLK 64
Query: 61 WTFHNELGLVFVAVYQRILHLLYVDDLLAMMKQSFSEIY 99
+ N+ LVFV +Q+IL L YVD L+ + + F + Y
Sbjct: 65 YKLDNQFELVFVVGFQKILTLTYVDKLIDDVHRLFRDKY 103
>pdb|3DMD|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3DMD|A Chain A, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3DMD|C Chain C, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3E70|C Chain C, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 32/102 (31%), Positives = 54/102 (52%), Gaps = 3/102 (2%)
Query: 334 DLEPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKLASFTRISSIVQAAMEEALVRI 393
D++ AL L+ L+ +VA E+ + L E + L GKK+ T I++ A++EA+ I
Sbjct: 51 DVDKALDELEIDLLEADVALEVVDALREKIKQKLVGKKVRIGTDKGKIIEEAVKEAVSEI 110
Query: 394 LTPRRSIDILRDVHAAKEQRKPYXXXXXXXXXXXKSTNLAKV 435
L R ID++ ++ A+ KPY K+T +AK+
Sbjct: 111 LETSRRIDLIEEIRKAE---KPYVIMFVGFNGSGKTTTIAKL 149
>pdb|3DM9|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 33/102 (32%), Positives = 55/102 (53%), Gaps = 3/102 (2%)
Query: 334 DLEPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKLASFTRISSIVQAAMEEALVRI 393
D++ AL L+ L+ +VA E+ + L E + L GKK+ T I++ A++EA+ I
Sbjct: 51 DVDKALDELEIDLLEADVALEVVDALREKIKQKLVGKKVRIGTDKGKIIEEAVKEAVSEI 110
Query: 394 LTPRRSIDILRDVHAAKEQRKPYXXXXXXXXXXXKSTNLAKV 435
L R ID++ ++ A+ KPY K+T +AK+
Sbjct: 111 LETSRRIDLIEEIRKAE---KPYVIXFVGFNGSGKTTTIAKL 149
>pdb|2IY3|A Chain A, Structure Of The E. Coli Signal Recognition Particle Bound
To A Translating Ribosome
Length = 432
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 39/82 (47%)
Query: 324 IAGKANLDKADLEPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKLASFTRISSIVQ 383
+ G+ + + DL+ L+ ++ LM +V E+A E V GK++ + ++
Sbjct: 16 LRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVIL 75
Query: 384 AAMEEALVRILTPRRSIDILRD 405
A + EAL L + +L+D
Sbjct: 76 ATVYEALKEALGGEARLPVLKD 97
>pdb|1O87|A Chain A, A New Mggdp Complex Of The Ffh Ng Domain
pdb|1O87|B Chain B, A New Mggdp Complex Of The Ffh Ng Domain
pdb|2C04|A Chain A, Gmppcp Complex Of Srp Gtpase Ffh Ng Domain At Ultra-High
Resolution
pdb|2C04|B Chain B, Gmppcp Complex Of Srp Gtpase Ffh Ng Domain At Ultra-High
Resolution
pdb|2J45|A Chain A, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
pdb|2J45|B Chain B, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
pdb|2J46|A Chain A, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
pdb|2J46|B Chain B, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
Length = 297
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 38/80 (47%)
Query: 326 GKANLDKADLEPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKLASFTRISSIVQAA 385
G+ + + DL+ L+ ++ LM +V E+A E V GK++ + ++ A
Sbjct: 18 GRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILAT 77
Query: 386 MEEALVRILTPRRSIDILRD 405
+ EAL L + +L+D
Sbjct: 78 VYEALKEALGGEARLPVLKD 97
>pdb|1JPJ|A Chain A, Gmppnp Complex Of Srp Gtpase Ng Domain
pdb|1JPN|A Chain A, Gmppnp Complex Of Srp Gtpase Ng Domain
pdb|1JPN|B Chain B, Gmppnp Complex Of Srp Gtpase Ng Domain
pdb|1RY1|U Chain U, Structure Of The Signal Recognition Particle Interacting
With The Elongation-Arrested Ribosome
Length = 296
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 38/80 (47%)
Query: 326 GKANLDKADLEPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKLASFTRISSIVQAA 385
G+ + + DL+ L+ ++ LM +V E+A E V GK++ + ++ A
Sbjct: 18 GRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILAT 77
Query: 386 MEEALVRILTPRRSIDILRD 405
+ EAL L + +L+D
Sbjct: 78 VYEALKEALGGEARLPVLKD 97
>pdb|1LS1|A Chain A, T. Aquaticus Ffh Ng Domain At 1.1a Resolution
Length = 295
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 38/80 (47%)
Query: 326 GKANLDKADLEPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKLASFTRISSIVQAA 385
G+ + + DL+ L+ ++ LM +V E+A E V GK++ + ++ A
Sbjct: 18 GRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILAT 77
Query: 386 MEEALVRILTPRRSIDILRD 405
+ EAL L + +L+D
Sbjct: 78 VYEALKEALGGEARLPVLKD 97
>pdb|3NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
pdb|3NG1|B Chain B, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
pdb|1OKK|A Chain A, Homo-Heterodimeric Complex Of The Srp Gtpases
pdb|2CNW|A Chain A, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|B Chain B, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|C Chain C, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2J7P|A Chain A, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
pdb|2J7P|B Chain B, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
pdb|1NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
pdb|2XKV|A Chain A, Atomic Model Of The Srp-Ftsy Early Conformation
Length = 294
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 38/80 (47%)
Query: 326 GKANLDKADLEPALKALKDRLMTKNVAEEIAEKLCESVAASLEGKKLASFTRISSIVQAA 385
G+ + + DL+ L+ ++ LM +V E+A E V GK++ + ++ A
Sbjct: 18 GRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILAT 77
Query: 386 MEEALVRILTPRRSIDILRD 405
+ EAL L + +L+D
Sbjct: 78 VYEALKEALGGEARLPVLKD 97
>pdb|2C03|A Chain A, Gdp Complex Of Srp Gtpase Ffh Ng Domain
pdb|2C03|B Chain B, Gdp Complex Of Srp Gtpase Ffh Ng Domain
Length = 297
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 11/97 (11%)
Query: 320 MFQSIA-----------GKANLDKADLEPALKALKDRLMTKNVAEEIAEKLCESVAASLE 368
MFQ ++ G+ + + DL+ L+ ++ LM +V E+ E V
Sbjct: 1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEAL 60
Query: 369 GKKLASFTRISSIVQAAMEEALVRILTPRRSIDILRD 405
GK++ + ++ A + EAL L + +L+D
Sbjct: 61 GKQVLESLTPAEVILATVYEALKEALGGEARLPVLKD 97
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
0.314 0.131 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,442,641
Number of Sequences: 62578
Number of extensions: 366204
Number of successful extensions: 865
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 850
Number of HSP's gapped (non-prelim): 13
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)