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= psy7980
(93 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2L05|A Chain A, Solution Nmr Structure Of The Ras-Binding Domain Of
SerineTHREONINE- Protein Kinase B-Raf From Homo
Sapiens, Northeast Structural Genomics Consortium
Target Hr4694f
Length = 95
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 7 PRGILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTG--VSLQWD 64
P+ ++R LPN+QRT V R G T+ ++L KA+ +R L PE C Y G + WD
Sbjct: 15 PQKPIVRVFLPNKQRTVVPARCGVTVRDSLKKALMMRGLIPECCAVYRIQDGEKKPIGWD 74
Query: 65 TDSDHLPTTEIRVEVME 81
TD L E+ VEV+E
Sbjct: 75 TDISWLTGEELHVEVLE 91
>pdb|3NY5|A Chain A, Crystal Structure Of The Rbd Domain Of
SerineTHREONINE-Protein Kinase B-Raf From Homo Sapiens.
Northeast Structural Genomics Consortium Target Hr4694f
pdb|3NY5|B Chain B, Crystal Structure Of The Rbd Domain Of
SerineTHREONINE-Protein Kinase B-Raf From Homo Sapiens.
Northeast Structural Genomics Consortium Target Hr4694f
pdb|3NY5|C Chain C, Crystal Structure Of The Rbd Domain Of
SerineTHREONINE-Protein Kinase B-Raf From Homo Sapiens.
Northeast Structural Genomics Consortium Target Hr4694f
pdb|3NY5|D Chain D, Crystal Structure Of The Rbd Domain Of
SerineTHREONINE-Protein Kinase B-Raf From Homo Sapiens.
Northeast Structural Genomics Consortium Target Hr4694f
Length = 96
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 33/80 (41%), Positives = 46/80 (57%), Gaps = 3/80 (3%)
Query: 11 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVS--LQWDTDSD 68
++R LPN+QRT V R G T+ ++L KA+ R L PE C Y G + WDTD
Sbjct: 15 IVRVFLPNKQRTVVPARCGVTVRDSLKKALXXRGLIPECCAVYRIQDGEKKPIGWDTDIS 74
Query: 69 HLPTTEIRVEVMEGNLALSS 88
L E+ VEV+E N+ L++
Sbjct: 75 WLTGEELHVEVLE-NVPLTT 93
>pdb|1RFA|A Chain A, Nmr Solution Structure Of The Ras-Binding Domain Of
C-Raf-1
Length = 79
Score = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 12 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY-----DSNTGVSLQWDTD 66
+R LPN+QRT V++R G +L + L KA+K+R L+PE C + L W+TD
Sbjct: 5 IRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTD 64
Query: 67 SDHLPTTEIRVEVME 81
+ L E++V+ ++
Sbjct: 65 AASLIGEELQVDFLD 79
>pdb|1RRB|A Chain A, The Ras-Binding Domain Of Raf-1 From Rat, Nmr, 1
Structure
Length = 107
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 12 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY-----DSNTGVSLQWDTD 66
+R LPN+QRT V++R G +L + L KA+K+R L+PE C + L W+TD
Sbjct: 21 IRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLQEHKGKKARLDWNTD 80
Query: 67 SDHLPTTEIRVEVME 81
+ L E++V+ ++
Sbjct: 81 AASLIGEELQVDFLK 95
>pdb|1C1Y|B Chain B, Crystal Structure Of Rap.Gmppnp In Complex With The Ras-
Binding-Domain Of C-Raf1 Kinase (Rafrbd)
Length = 77
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 12 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY-----DSNTGVSLQWDTD 66
+R LPN+QRT V++R G +L + L KA+K+R L+PE C + L W+TD
Sbjct: 4 IRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTD 63
Query: 67 SDHLPTTEIRVEVM 80
+ L E++V+ +
Sbjct: 64 AASLIGEELQVDFL 77
>pdb|1GUA|B Chain B, Human Rap1a, Residues 1-167, Double Mutant (E30d,K31e)
Complexed With Gppnhp And The Ras-Binding-Domain Of
Human C-Raf1, Residues 51-131
Length = 81
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 12 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY-----DSNTGVSLQWDTD 66
+R LPN+QRT V++R G +L + L KA+K+R L+PE C + L W+TD
Sbjct: 8 IRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTD 67
Query: 67 SDHLPTTEIRVEVM 80
+ L E++V+ +
Sbjct: 68 AASLIGEELQVDFL 81
>pdb|3KUD|B Chain B, Complex Of Ras-Gdp With Rafrbd(A85k)
Length = 81
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 5/74 (6%)
Query: 12 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY-----DSNTGVSLQWDTD 66
+R LPN+QRT V++R G +L + L K +K+R L+PE C + L W+TD
Sbjct: 8 IRVFLPNKQRTVVNVRNGMSLHDCLMKKLKVRGLQPECCAVFRLLHEHKGKKARLDWNTD 67
Query: 67 SDHLPTTEIRVEVM 80
+ L E++V+ +
Sbjct: 68 AASLIGEELQVDFL 81
>pdb|3KUC|B Chain B, Complex Of Rap1a(E30dK31E)GDP WITH RAFRBD(A85KN71R)
Length = 81
Score = 52.8 bits (125), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 5/74 (6%)
Query: 12 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY-----DSNTGVSLQWDTD 66
+R LPN+QRT V +R G +L + L K +K+R L+PE C + L W+TD
Sbjct: 8 IRVFLPNKQRTVVRVRNGMSLHDCLMKKLKVRGLQPECCAVFRLLHEHKGKKARLDWNTD 67
Query: 67 SDHLPTTEIRVEVM 80
+ L E++V+ +
Sbjct: 68 AASLIGEELQVDFL 81
>pdb|1WXM|A Chain A, Solution Structure Of The N-Terminal Ras-Binding Domain
(Rbd) In Human A-Raf Kinase
Length = 86
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 12 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTG--VSLQWDTDSDH 69
++ LPN+QRT V +R G ++ ++L KA+K+R L + C Y G WDT
Sbjct: 10 VKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYRLIKGRKTVTAWDTAIAP 69
Query: 70 LPTTEIRVEVMEG 82
L E+ VEV+ G
Sbjct: 70 LDGEELIVEVLSG 82
>pdb|3HAZ|A Chain A, Crystal Structure Of Bifunctional Proline Utilization A
(Puta) Protein
pdb|3HAZ|B Chain B, Crystal Structure Of Bifunctional Proline Utilization A
(Puta) Protein
Length = 1001
Score = 28.1 bits (61), Expect = 1.3, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 33/74 (44%)
Query: 16 LPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEI 75
LP++ SV + EA+S+A + L P++ L + D++ E+
Sbjct: 230 LPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLEL 289
Query: 76 RVEVMEGNLALSSL 89
++V+ LA SL
Sbjct: 290 SLDVIAATLADPSL 303
>pdb|2Q5T|A Chain A, Full-Length Cholix Toxin From Vibrio Cholerae
pdb|3Q9O|A Chain A, Full-Length Cholix Toxin From Vibrio Cholerae In Complex
With Nad
Length = 642
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 14/59 (23%)
Query: 15 QLPNQQRTSVHIRKGQTL------------LEALSKAMKLRNLKPEMCTAYDSNTGVSL 61
Q P +QR +H KG + LE L+++ K R+L ++ AY + VSL
Sbjct: 262 QKPVEQR--IHFSKGNAMSALAAHRVCGVPLETLARSRKPRDLTDDLSCAYQAQNIVSL 318
>pdb|4FN5|A Chain A, Elongation Factor G 1 (Pseudomonas Aeruginosa) In Complex
With Argyrin B
Length = 709
Score = 26.9 bits (58), Expect = 3.1, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 25 HIRKGQTLLEALSKAMKLRNLK----PEMCTAYDSNTGVSLQWDTDSDHLPT-TEI 75
++ +G+ + + ++LR L P +C + N GV L D D+LP TEI
Sbjct: 240 YLEEGELSEAEIKEGLRLRTLACEIVPAVCGSSFKNKGVPLVLDAVIDYLPAPTEI 295
>pdb|2XEX|A Chain A, Crystal Structure Of Staphylococcus Aureus Elongation
Factor G
pdb|2XEX|B Chain B, Crystal Structure Of Staphylococcus Aureus Elongation
Factor G
Length = 693
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 32 LLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPT 72
L EA+ +A P +C N GV L D D+LP+
Sbjct: 240 LKEAIRQATTNVEFYPVLCGTAFKNKGVQLMLDAVIDYLPS 280
>pdb|3ZZU|A Chain A, Crystal Structure Of Staphylococcus Aureus Elongation
Factor G With Mutations M16i And F88l
pdb|3ZZU|B Chain B, Crystal Structure Of Staphylococcus Aureus Elongation
Factor G With Mutations M16i And F88l
Length = 693
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 32 LLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPT 72
L EA+ +A P +C N GV L D D+LP+
Sbjct: 240 LKEAIRQATTNVEFYPVLCGTAFKNKGVQLMLDAVIDYLPS 280
>pdb|3ZZT|A Chain A, Crystal Structure Of Staphylococcus Aureus Elongation
Factor G With A Fusidic-Acid-Resistant Mutation F88l
pdb|3ZZT|B Chain B, Crystal Structure Of Staphylococcus Aureus Elongation
Factor G With A Fusidic-Acid-Resistant Mutation F88l
Length = 693
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 32 LLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPT 72
L EA+ +A P +C N GV L D D+LP+
Sbjct: 240 LKEAIRQATTNVEFYPVLCGTAFKNKGVQLMLDAVIDYLPS 280
>pdb|3ZZ0|A Chain A, Crystal Structure Of Ribosomal Elongation Factor (Ef)-G
From Staphylococcus Aureus With A Fusidic Acid
Hyper-Sensitivity Mutation M16i
pdb|3ZZ0|B Chain B, Crystal Structure Of Ribosomal Elongation Factor (Ef)-G
From Staphylococcus Aureus With A Fusidic Acid
Hyper-Sensitivity Mutation M16i
Length = 693
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 32 LLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPT 72
L EA+ +A P +C N GV L D D+LP+
Sbjct: 240 LKEAIRQATTNVEFYPVLCGTAFKNKGVQLMLDAVIDYLPS 280
>pdb|4EQB|A Chain A, 1.5 Angstrom Crystal Structure Of SpermidinePUTRESCINE
ABC Transporter Substrate-Binding Protein From
Streptococcus Pneumoniae Strain Canada Mdr_19a In
Complex With Calcium And Hepes.
pdb|4EQB|B Chain B, 1.5 Angstrom Crystal Structure Of SpermidinePUTRESCINE
ABC Transporter Substrate-Binding Protein From
Streptococcus Pneumoniae Strain Canada Mdr_19a In
Complex With Calcium And Hepes
Length = 330
Score = 26.2 bits (56), Expect = 4.4, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 45 LKPEMCTAYDSNTGVSLQWDT-DSDHLPTTEIR 76
+ PE+ T + TG+ +Q++T DS+ T+I+
Sbjct: 20 IDPELLTQFTEETGIQVQYETFDSNEAMYTKIK 52
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 0.132 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,392,620
Number of Sequences: 62578
Number of extensions: 72854
Number of successful extensions: 178
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 162
Number of HSP's gapped (non-prelim): 17
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)