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= 005305
(703 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 37.0 bits (84), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 62/148 (41%), Gaps = 36/148 (24%)
Query: 315 EALDLYYEMRDSGVKMDHFTFSMIIRICTRLASLEHAKQAHAGLVRHGFGLDIVANSALV 374
EAL LY E R +GV++ + +++++ +C+ LA + GL R G DI
Sbjct: 44 EALRLYDEARRNGVQLSQYHYNVLLYVCS-LAEAATESSPNPGLSR---GFDI------- 92
Query: 375 DFYSKWGRIEDARHVFDKMLCKNVISWNALIAGYGNHGR-------GEEAVELFEQMLLN 427
F +M+ V+ A + N R E A ++ +QM
Sbjct: 93 ---------------FKQMIVDKVVPNEAT---FTNGARLAVAKDDPEMAFDMVKQMKAF 134
Query: 428 GMRPNHVTFLAVLSACSRSGLSERGWEI 455
G++P ++ L R G +++ +E+
Sbjct: 135 GIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 33.5 bits (75), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 30/141 (21%), Positives = 57/141 (40%), Gaps = 22/141 (15%)
Query: 315 EALDLYYEMRDSGVKMDHFTFSMIIRICTRLASLEHAKQAHAGLVRHGFGLDIVANSALV 374
EAL LY E R +GV++ + +++++ +C+ LA + GL R G DI
Sbjct: 44 EALRLYDEARRNGVQLSQYHYNVLLYVCS-LAEAATESSPNPGLSR---GFDIF------ 93
Query: 375 DFYSKWGRIEDARHVFDKMLCKNVISWNALIAGYGNHGRGEEAVELFEQMLLNGMRPNHV 434
+ + DK++ N E A + +Q G++P
Sbjct: 94 -----------KQXIVDKVVPNEATFTNGARLAVAKDD-PEXAFDXVKQXKAFGIQPRLR 141
Query: 435 TFLAVLSACSRSGLSERGWEI 455
++ L R G +++ +E+
Sbjct: 142 SYGPALFGFCRKGDADKAYEV 162
>pdb|3SYV|A Chain A, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|B Chain B, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|C Chain C, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|D Chain D, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|E Chain E, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|F Chain F, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|G Chain G, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|H Chain H, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
Length = 347
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/116 (23%), Positives = 45/116 (38%), Gaps = 2/116 (1%)
Query: 490 ALIRGAPFKTTKNMWAALLTACRVNGNLELGKFAAEKLYGMEPEKLSNYVVLLNIYNSSG 549
A+ +G + T + W A TA L L EKL+G + E++ + G
Sbjct: 73 AVEKGPQYGTLEKAWHAFFTAAERLSELHLE--VREKLHGPDSERVRTWQRGAFHRQVLG 130
Query: 550 KLKEAAEVIRTLRRKGLRMLPACSWIEVKKQPHVFLSGDQSHVQTKEIYRKVDRMM 605
+E+ R+ L +E K+ + D+ QT+E + K D M
Sbjct: 131 GFRESRAAEDGFRKAQKPWLKRLKEVEASKKSYHTARKDEKTAQTRESHAKADSSM 186
>pdb|3QE6|A Chain A, Mouse Pacsin 3 F-Bar Domain Structure
pdb|3QE6|B Chain B, Mouse Pacsin 3 F-Bar Domain Structure
Length = 304
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 27/116 (23%), Positives = 45/116 (38%), Gaps = 2/116 (1%)
Query: 490 ALIRGAPFKTTKNMWAALLTACRVNGNLELGKFAAEKLYGMEPEKLSNYVVLLNIYNSSG 549
A+ +G + T + W A TA L L EKL+G + E++ + G
Sbjct: 67 AVEKGPQYGTLEKAWHAFFTAAERLSELHLE--VREKLHGPDSERVRTWQRGAFHRPVLG 124
Query: 550 KLKEAAEVIRTLRRKGLRMLPACSWIEVKKQPHVFLSGDQSHVQTKEIYRKVDRMM 605
+E+ R+ L +E K+ + D+ QT+E + K D M
Sbjct: 125 GFRESRAAEDGFRKAQKPWLKRLKEVEASKKSYHTARKDEKTAQTRESHAKADSSM 180
>pdb|3M3W|A Chain A, Crystal Strcuture Of Mouse Pacsin3 Bar Domain Mutant
pdb|3M3W|B Chain B, Crystal Strcuture Of Mouse Pacsin3 Bar Domain Mutant
Length = 320
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 14/122 (11%)
Query: 490 ALIRGAPFKTTKNMWAALLTACRVNGNLELGKFAAEKLYGMEPEKLSNYV------VLLN 543
A+ +G + T + W A TA L L EKL+G + E++ + +L
Sbjct: 67 AVEKGPQYGTLEKAWHAFFTAAERLSELHLE--VREKLHGPDSERVRTWQRGAFHRPVLG 124
Query: 544 IYNSSGKLKEAAEVIRTLRRKGLRMLPACSWIEVKKQPHVFLSGDQSHVQTKEIYRKVDR 603
+ +S + A + R ++ L+ L +E K+ + D+ QT+E + K D
Sbjct: 125 GFRAS---RAAEDGFRKAQKPWLKRLKE---VEASKKSYHTARKDEKTAQTRESHAKADS 178
Query: 604 MM 605
M
Sbjct: 179 SM 180
>pdb|2V3C|C Chain C, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
pdb|2V3C|D Chain D, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
Length = 432
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 63/126 (50%), Gaps = 29/126 (23%)
Query: 526 KLYGMEPEKLS-----NYVVLLNIYNSSGKLKEAAEVIRTLRRKGLRMLPA--------- 571
KL G E +KL V+LL SGK AA++ R ++++GL+ PA
Sbjct: 83 KLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLK--PALIAADTYRP 140
Query: 572 CSWIEVKK---QPHVFLSGDQSHVQTK--------EIYRKVDRMMLEISKHGYVPEEKTL 620
++ ++K+ + HV + GD++ ++ E ++K D ++++ + G EEK L
Sbjct: 141 AAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTA--GRHKEEKGL 198
Query: 621 LPDVDE 626
L ++ +
Sbjct: 199 LEEMKQ 204
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 63/126 (50%), Gaps = 29/126 (23%)
Query: 526 KLYGMEPEKLS-----NYVVLLNIYNSSGKLKEAAEVIRTLRRKGLRMLPA--------- 571
KL G E +KL V+LL SGK AA++ R ++++GL+ PA
Sbjct: 83 KLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLK--PALIAADTYRP 140
Query: 572 CSWIEVKK---QPHVFLSGDQSHVQTK--------EIYRKVDRMMLEISKHGYVPEEKTL 620
++ ++K+ + HV + GD++ ++ E ++K D ++++ + G EEK L
Sbjct: 141 AAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTA--GRHKEEKGL 198
Query: 621 LPDVDE 626
L ++ +
Sbjct: 199 LEEMKQ 204
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 0.137 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,907,455
Number of Sequences: 62578
Number of extensions: 782711
Number of successful extensions: 1581
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1577
Number of HSP's gapped (non-prelim): 8
length of query: 703
length of database: 14,973,337
effective HSP length: 106
effective length of query: 597
effective length of database: 8,340,069
effective search space: 4979021193
effective search space used: 4979021193
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: 55 (25.8 bits)