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= 028867
(202 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1CT9|A Chain A, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
pdb|1CT9|B Chain B, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
pdb|1CT9|C Chain C, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
pdb|1CT9|D Chain D, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
Length = 553
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 51/113 (45%), Gaps = 15/113 (13%)
Query: 85 GSLNNLCSLIRQYG----LSKGTD-EAMFVIEAYRTLRDRGPYPADQVVKDLDGSFAFVV 139
G + N +L +YG G+D E + + +++GP + + DL G FAF +
Sbjct: 75 GEIYNHQALRAEYGDRYQFQTGSDCEVILAL-----YQEKGP----EFLDDLQGMFAFAL 125
Query: 140 YDSKAGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKEGCAKSFAPFPQG 192
YDS+ G + LY G G + ++ +++ + C ++ FP G
Sbjct: 126 YDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVC-RTIKEFPAG 177
>pdb|1C5K|A Chain A, The Structure Of Tolb, An Essential Component Of The Tol-
Dependent Translocation System And Its Interactions With
The Translocation Domain Of Colicin E9
pdb|2IVZ|A Chain A, Structure Of Tolb In Complex With A Peptide Of The Colicin
E9 T-Domain
pdb|2IVZ|B Chain B, Structure Of Tolb In Complex With A Peptide Of The Colicin
E9 T-Domain
pdb|2IVZ|C Chain C, Structure Of Tolb In Complex With A Peptide Of The Colicin
E9 T-Domain
pdb|2IVZ|D Chain D, Structure Of Tolb In Complex With A Peptide Of The Colicin
E9 T-Domain
Length = 439
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 112 AYRTLRDRGPYPADQVVKDLDGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVI 171
AY + G +P + V D DG FVV+ S + A DG Y + S ++
Sbjct: 169 AYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALV 228
Query: 172 SDDLEVIKEGCAKSFAPFPQ 191
++ + G + A FP+
Sbjct: 229 ---IQTLANGAVRQVASFPR 245
>pdb|3IAX|A Chain A, The Crystal Structure Of The Tolb Box Of Colicin A In
Complex With Tolb Reveals Important Differences In The
Recruitment Of The Common Tolb Translocation Portal Used
By Group A Colicins
Length = 438
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 112 AYRTLRDRGPYPADQVVKDLDGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVI 171
AY + G +P + V D DG FVV+ S + A DG Y + S ++
Sbjct: 168 AYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALV 227
Query: 172 SDDLEVIKEGCAKSFAPFPQ 191
++ + G + A FP+
Sbjct: 228 ---IQTLANGAVRQVASFPR 244
>pdb|2HQS|A Chain A, Crystal Structure Of TolbPAL COMPLEX
pdb|2HQS|B Chain B, Crystal Structure Of TolbPAL COMPLEX
pdb|2HQS|D Chain D, Crystal Structure Of TolbPAL COMPLEX
pdb|2HQS|F Chain F, Crystal Structure Of TolbPAL COMPLEX
Length = 415
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 112 AYRTLRDRGPYPADQVVKDLDGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVI 171
AY + G +P + V D DG FVV+ S + A DG Y + S ++
Sbjct: 147 AYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALV 206
Query: 172 SDDLEVIKEGCAKSFAPFPQ 191
++ + G + A FP+
Sbjct: 207 ---IQTLANGAVRQVASFPR 223
>pdb|2W8B|A Chain A, Crystal Structure Of Processed Tolb In Complex With Pal
Length = 409
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 112 AYRTLRDRGPYPADQVVKDLDGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVI 171
AY + G +P + V D DG FVV+ S + A DG Y + S ++
Sbjct: 147 AYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALV 206
Query: 172 SDDLEVIKEGCAKSFAPFPQ 191
++ + G + A FP+
Sbjct: 207 ---IQTLANGAVRQVASFPR 223
>pdb|2W8B|B Chain B, Crystal Structure Of Processed Tolb In Complex With Pal
pdb|2W8B|D Chain D, Crystal Structure Of Processed Tolb In Complex With Pal
pdb|2W8B|F Chain F, Crystal Structure Of Processed Tolb In Complex With Pal
Length = 409
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 112 AYRTLRDRGPYPADQVVKDLDGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVI 171
AY + G +P + V D DG FVV+ S + A DG Y + S ++
Sbjct: 147 AYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALV 206
Query: 172 SDDLEVIKEGCAKSFAPFPQ 191
++ + G + A FP+
Sbjct: 207 ---IQTLANGAVRQVASFPR 223
>pdb|2W4B|A Chain A, Epstein-Barr Virus Alkaline Nuclease D203s Mutant
pdb|2W4B|B Chain B, Epstein-Barr Virus Alkaline Nuclease D203s Mutant
Length = 470
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 43/185 (23%), Positives = 60/185 (32%), Gaps = 54/185 (29%)
Query: 33 DTLSDFLSRHSDNTFSMNFGHAAVLAYV-----PPHSPLTKDRRLFCGFEDI-------- 79
D L D + + TF+ A+V PP P + L+C + I
Sbjct: 5 DELEDPMEEMTSYTFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQEFSGETG 64
Query: 80 YCLFMGSL------NNLCSLIRQY-GLSKGTDEAMFVIEAYRTLRDRGPYPADQVVKDLD 132
+C F+ SL + SL Y GL + TDE V+ +Y RG
Sbjct: 65 FCDFVSSLVQENDSKDGPSLKSIYWGLQEATDEQRTVLCSYVESMTRG------------ 112
Query: 133 GSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKEGCAKSFAPFPQG 192
L W I +G + S L IK G K F P P
Sbjct: 113 ----------------------QSENLMWDILRNGIISSSKLLSTIKNGPTKVFEPAPIS 150
Query: 193 KLNFF 197
++F
Sbjct: 151 TNHYF 155
>pdb|2W45|A Chain A, Epstein-Barr Virus Alkaline Nuclease
pdb|2W45|B Chain B, Epstein-Barr Virus Alkaline Nuclease
Length = 470
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 43/185 (23%), Positives = 60/185 (32%), Gaps = 54/185 (29%)
Query: 33 DTLSDFLSRHSDNTFSMNFGHAAVLAYV-----PPHSPLTKDRRLFCGFEDI-------- 79
D L D + + TF+ A+V PP P + L+C + I
Sbjct: 5 DELEDPMEEMTSYTFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQEFSGETG 64
Query: 80 YCLFMGSL------NNLCSLIRQY-GLSKGTDEAMFVIEAYRTLRDRGPYPADQVVKDLD 132
+C F+ SL + SL Y GL + TDE V+ +Y RG
Sbjct: 65 FCDFVSSLVQENDSKDGPSLKSIYWGLQEATDEQRTVLCSYVESMTRG------------ 112
Query: 133 GSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKEGCAKSFAPFPQG 192
L W I +G + S L IK G K F P P
Sbjct: 113 ----------------------QSENLMWDILRNGIISSSKLLSTIKNGPTKVFEPAPIS 150
Query: 193 KLNFF 197
++F
Sbjct: 151 TNHYF 155
>pdb|1CRZ|A Chain A, Crystal Structure Of The E. Coli Tolb Protein
Length = 403
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 3/80 (3%)
Query: 112 AYRTLRDRGPYPADQVVKDLDGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVI 171
AY + G +P + V D DG FVV+ S A DG Y + S ++
Sbjct: 141 AYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLXSPAWSPDGSKLAYVTFESGRSALV 200
Query: 172 SDDLEVIKEGCAKSFAPFPQ 191
++ + G + A FP+
Sbjct: 201 ---IQTLANGAVRQVASFPR 217
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
0.322 0.139 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,506,797
Number of Sequences: 62578
Number of extensions: 266406
Number of successful extensions: 556
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 553
Number of HSP's gapped (non-prelim): 10
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)