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= 028756
(204 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KKJ|A Chain A, X-Ray Structure Of P. Syringae Q888a4 Oxidoreductase At
Resolution 2.5a, Northeast Structural Genomics
Consortium Target Psr10
pdb|3KKJ|B Chain B, X-Ray Structure Of P. Syringae Q888a4 Oxidoreductase At
Resolution 2.5a, Northeast Structural Genomics
Consortium Target Psr10
Length = 336
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 44/169 (26%), Positives = 74/169 (43%), Gaps = 23/169 (13%)
Query: 16 FDHGAPFFTVTNNDVLALVREWESGGLVAEWKVNLGSFD--RVSKKFVNIQQDGMNKKYV 73
D GA +FT + V++W++ G VAEW L +F R+S ++V
Sbjct: 51 LDXGAQYFTARDRRFATAVKQWQAQGHVAEWTPLLYNFHAGRLSPS------PDEQVRWV 104
Query: 74 GVPGMNSICKALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDGQSLGQFNGVVASDKN 133
G PG ++I +A V + E + W++ +GQ+ G F+ V+
Sbjct: 105 GKPGXSAITRAXRGDXPVSFSCRI----TEVFRGEEHWNLLDAEGQNHGPFSHVI----- 155
Query: 134 VVSPRFRDVTGRPPPLDLTFAPDLAVKLEEIPVNPCFALMLAFSEPLSS 182
+ +P + T L AP LA + + +P +A+ LAF PL +
Sbjct: 156 IATPAPQAST------LLAAAPKLASVVAGVKXDPTWAVALAFETPLQT 198
>pdb|2XTL|A Chain A, Structure Of The Major Pilus Backbone Protein From
Streptococcus Agalactiae
pdb|2XTL|B Chain B, Structure Of The Major Pilus Backbone Protein From
Streptococcus Agalactiae
Length = 452
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 32/119 (26%), Positives = 45/119 (37%), Gaps = 6/119 (5%)
Query: 6 ETSEDGNEMLFDHGAPFFTVTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFVNIQQ 65
+T++DG E L GA F + LA +SG K + S V
Sbjct: 274 KTNKDGKERL--AGATFLVKKDGKYLAR----KSGVATDAEKAAVDSTKSALDAAVKAYN 327
Query: 66 DGMNKKYVGVPGMNSICKALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDGQSLGQF 124
D +K G G +++ Q F +EW+EDKN +V L GQF
Sbjct: 328 DLTKEKQEGQDGKSALATVSEKQKAYNDAFVKANYSYEWVEDKNAKNVVKLISNDKGQF 386
>pdb|3T58|A Chain A, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
pdb|3T58|B Chain B, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
pdb|3T58|C Chain C, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
pdb|3T58|D Chain D, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
pdb|3T59|A Chain A, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
pdb|3T59|B Chain B, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
pdb|3T59|C Chain C, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
pdb|3T59|D Chain D, C76aC455S MUTANT OF MOUSE QSOX1 CONTAINING AN INTERDOMAIN
DISULFIDE
Length = 519
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 22 FFTVTNNDVLALVREWESGGLVAEWKVNLGSFDRVS-KKFVNIQQDGMNK 70
FFT D LALV E E L E ++L + V+ ++ +N + D +NK
Sbjct: 151 FFTRNKADYLALVFEREDSYLGREVTLDLSQYHAVAVRRVLNTESDLVNK 200
>pdb|2NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 293
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 21 ITEEDLKATLREIRRALMDAD--VNL----EVTRDFVERVREEALGKQVLESLTPAEVIL 74
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 75 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 107
>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 = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVARDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 21 ITEEDLKATLREIRRALMDAD--VNL----EVTRDFVERVREEALGKQVLESLTPAEVIL 74
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 75 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 107
>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 = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVTRDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVTRDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>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 = 1.7, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVARDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>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 = 1.7, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVARDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>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 = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVTRDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>pdb|1LS1|A Chain A, T. Aquaticus Ffh Ng Domain At 1.1a Resolution
Length = 295
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVARDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>pdb|2BPA|1 Chain 1, Atomic Structure Of Single-Stranded Dna Bacteriophage
Phix174 And Its Functional Implications
pdb|1AL0|F Chain F, Procapsid Of Bacteriophage Phix174
Length = 426
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 109 NLWS----VSGLDGQSLGQFNGVVASDKNVVSPRF 139
NLW+ V G D SLGQF+G V PRF
Sbjct: 241 NLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRF 275
>pdb|1CD3|F Chain F, Procapsid Of Bacteriophage Phix174
Length = 426
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 109 NLWS----VSGLDGQSLGQFNGVVASDKNVVSPRF 139
NLW+ V G D SLGQF+G V PRF
Sbjct: 241 NLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRF 275
>pdb|2IY3|A Chain A, Structure Of The E. Coli Signal Recognition Particle Bound
To A Translating Ribosome
Length = 432
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 25 VTNNDVLALVREWESGGLVAEWKVNLGSFDRVSKKFV-NIQQDGMNKKYVGVPGMNSICK 83
+T D+ A +RE + A+ VNL V++ FV ++++ + K+ + +
Sbjct: 22 ITEEDLKATLREIRRALMDAD--VNL----EVARDFVERVREEALGKQVLESLTPAEVIL 75
Query: 84 ALCHQPGVESKFGVGVGRFEWLEDKNLWSVSGLDG 118
A ++ ++ G G R L+D+NLW + GL G
Sbjct: 76 ATVYE-ALKEALG-GEARLPVLKDRNLWFLVGLQG 108
>pdb|1KVP|A Chain A, Structural Analysis Of The Spiroplasma Virus, Spv4,
Implications For Evolutionary Variation To Obtain Host
Diversity Among The Microviridae, Electron Microscopy,
Alpha Carbons Only
Length = 497
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 109 NLWS----VSGLDGQSLGQFNGVVASDKNVVSPRF 139
NLW+ V G D SLGQF+G V PRF
Sbjct: 312 NLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRF 346
>pdb|1GFF|1 Chain 1, The Atomic Structure Of The Degraded Procapsid Particle Of
The Bacteriophage G4: Induced Structural Changes In The
Presence Of Calcium Ions And Functional Implications
Length = 426
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 111 WSVSGLDGQSLGQFNGVVASDKNVVSPRF 139
+ V G D SLGQF+G V N PRF
Sbjct: 247 YDVDGTDQSSLGQFSGRVQQTFNHKVPRF 275
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
0.319 0.138 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,703,096
Number of Sequences: 62578
Number of extensions: 286316
Number of successful extensions: 619
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 615
Number of HSP's gapped (non-prelim): 18
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)