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= 044604
(476 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ODF|A Chain A, Structure Of Ygr205w Protein
Length = 290
Score = 135 bits (340), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 99/266 (37%), Positives = 134/266 (50%), Gaps = 23/266 (8%)
Query: 228 YLPWWY---------IGFSAPQGCGK--TTLAFALDYLFRVTGRKS-ATISIDDFYLTAE 275
Y+P W+ I FS PQG GK T++ + + G KS SIDDFYLT E
Sbjct: 19 YIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHE 78
Query: 276 GQAKLREANRGNALLEFRGNAGSHDLQLSVETLTAISKLTK--EGTKMKLPRYDKSAYNG 333
Q KL E + N LL+ RG G+HD++L E L I + + + LP+YDKS + G
Sbjct: 79 DQLKLNEQFKNNKLLQGRGLPGTHDMKLLQEVLNTIFNNNEHPDQDTVVLPKYDKSQFKG 138
Query: 334 RGDRADPSTWPEIEGPLTVVLYEGWMLGFKPL--PVEVVKAVDPQLETVNKNLEAYFD-A 390
GDR T +I+ P+ + + EGW LGF P+ +E + + VN L Y D
Sbjct: 139 EGDRC--PTGQKIKLPVDIFILEGWFLGFNPILQGIENNDLLTGDMVDVNAKLFFYSDLL 196
Query: 391 W-DKFIKAW-IVIKIKDPSCVYEWRLQAEIAMREAGNPGMSDEEVKDFVSRYLPAYHAYL 448
W + IK+ IV + + VY WRLQ E + GM+DE+V FV RY+P+Y YL
Sbjct: 197 WRNPEIKSLGIVFTTDNINNVYGWRLQQEHELISKVGKGMTDEQVHAFVDRYMPSYKLYL 256
Query: 449 PTLYSEGPNGSDPEHTLIIEIDDGRN 474
GS TL + ID RN
Sbjct: 257 NDFVRSESLGSIA--TLTLGIDSNRN 280
>pdb|3ASY|A Chain A, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASY|B Chain B, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|A Chain A, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|B Chain B, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
Length = 211
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 39/129 (30%), Positives = 56/129 (43%), Gaps = 20/129 (15%)
Query: 232 WYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALLE 291
+ IG + GKTTLA AL R G + A + +D +Y G L E R N
Sbjct: 7 FVIGIAGGTASGKTTLAQALA---RTLGERVALLPMDHYYKDL-GHLPLEERLRVNY--- 59
Query: 292 FRGNAGSHDLQLSVETLTAISKLTKEGTKMKLPRYDKSAYNGRGDRADPSTWPEIEGPLT 351
+ + DL L +E A+ + G +++P YD AY R R P P
Sbjct: 60 --DHPDAFDLALYLEHAQALLR----GLPVEMPVYDFRAYT-RSPRRTPVR------PAP 106
Query: 352 VVLYEGWML 360
VV+ EG ++
Sbjct: 107 VVILEGILV 115
>pdb|2IY3|A Chain A, Structure Of The E. Coli Signal Recognition Particle Bound
To A Translating Ribosome
Length = 432
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
>pdb|2FFH|A Chain A, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
pdb|2FFH|B Chain B, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
pdb|2FFH|C Chain C, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
Length = 425
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
>pdb|2VC9|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With 2-Acetamido-1,2-Dideoxynojirmycin
pdb|2VCA|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With Beta-N-Acetyl-D-Glucosamine
pdb|2VCB|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With Pugnac
pdb|2VCC|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
Length = 891
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 415 QAEIAMREAGNPGMSDEEVKDFVSRYLPAYHAYL 448
Q E+ R G SDEEVK+F+S PAY A+
Sbjct: 311 QEEVLRRTLNEFGYSDEEVKEFISG--PAYFAWF 342
>pdb|4A4A|A Chain A, Cpgh89 (E483q, E601q), From Clostridium Perfringens, In
Complex With Its Substrate Glcnac-Alpha-1,4-Galactose
Length = 914
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 415 QAEIAMREAGNPGMSDEEVKDFVSRYLPAYHAYL 448
Q E+ R G SDEEVK+F+S PAY A+
Sbjct: 334 QEEVLRRTLNEFGYSDEEVKEFISG--PAYFAWF 365
>pdb|2NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 293
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 100 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 156
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 157 EVMDGESPESIRRRVE 172
>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 = 4.3, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
>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 = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
>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 = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
>pdb|1RJ9|B Chain B, Structure Of The Heterodimer Of The Conserved Gtpase
Domains Signal Recognition Particle (Ffh) And Its
Receptor (Ftsy)
Length = 300
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
>pdb|1FFH|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 294
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 100 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 156
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 157 EVMDGESPESIRRRVE 172
>pdb|1LS1|A Chain A, T. Aquaticus Ffh Ng Domain At 1.1a Resolution
Length = 295
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
>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 = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 231 WWYIGFSAPQGCGKTTLAFALDYLFRVTGRKSATISIDDFYLTAEGQAKLREANRGNALL 290
W+ +G QG GKTT A L ++ GR+ ++ D A Q +L G +L
Sbjct: 101 WFLVGL---QGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 157
Query: 291 EFRGNAGSHDLQLSVE 306
E ++ VE
Sbjct: 158 EVMDGESPESIRRRVE 173
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 0.134 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,095,210
Number of Sequences: 62578
Number of extensions: 567388
Number of successful extensions: 1377
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1361
Number of HSP's gapped (non-prelim): 16
length of query: 476
length of database: 14,973,337
effective HSP length: 102
effective length of query: 374
effective length of database: 8,590,381
effective search space: 3212802494
effective search space used: 3212802494
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: 53 (25.0 bits)