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= 010297
(513 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J53|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The
Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 8.5
pdb|1J54|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The
Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 5.8
pdb|2IDO|A Chain A, Structure Of The E. Coli Pol Iii Epsilon-Hot Proofreading
Complex
pdb|2IDO|C Chain C, Structure Of The E. Coli Pol Iii Epsilon-Hot Proofreading
Complex
pdb|2XY8|A Chain A, Paramagnetic-Based Nmr Structure Of The Complex Between
The N-Terminal Epsilon Domain And The Theta Domain Of
The Dna Polymerase Iii
Length = 186
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 62/138 (44%), Gaps = 15/138 (10%)
Query: 13 FDVETTVPTRPGQRF---AILEFGAILVCPKKL--EELHNYSTLVRPADPELISSLSVRC 67
D ETT + G + I+E GA+ V ++L H Y R DPE +
Sbjct: 11 LDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPE-----AFGV 65
Query: 68 NGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPK-- 125
+GI + ++ PTFA++AD D + G HN FD + F+ + R P+
Sbjct: 66 HGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTF 124
Query: 126 -GTIDSLALLTQRF-GRR 141
DSLA+ + F G+R
Sbjct: 125 CKVTDSLAVARKMFPGKR 142
>pdb|2GUI|A Chain A, Structure And Function Of Cyclized Versions Of The
Proofread Exonuclease Subunit Of E. Coli Dna Polymerase
Iii
Length = 194
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 61/138 (44%), Gaps = 15/138 (10%)
Query: 13 FDVETTVPTRPGQRF---AILEFGAILVCPKKL--EELHNYSTLVRPADPELISSLSVRC 67
D ETT + G + I+E GA+ V ++L H Y R DPE
Sbjct: 14 LDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFG-----V 68
Query: 68 NGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPK-- 125
+GI + ++ PTFA++AD D + G HN FD + F+ + R P+
Sbjct: 69 HGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTF 127
Query: 126 -GTIDSLALLTQRF-GRR 141
DSLA+ + F G+R
Sbjct: 128 CKVTDSLAVARKMFPGKR 145
>pdb|1ZBH|A Chain A, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
pdb|1ZBH|B Chain B, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
pdb|1ZBH|C Chain C, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
pdb|1ZBH|D Chain D, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
Length = 299
Score = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 2/85 (2%)
Query: 10 IAFFDVETTVPTRPGQRFA--ILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRC 67
I D E T F I+EF +L+ LE + VRP +S +
Sbjct: 80 ICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISL 139
Query: 68 NGITPDAVVSSPTFADIADTVFDIL 92
GIT D V + TF + V D++
Sbjct: 140 TGITQDQVDRADTFPQVLKKVIDLM 164
>pdb|2P1J|A Chain A, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
pdb|2P1J|B Chain B, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
Length = 186
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 66/148 (44%), Gaps = 11/148 (7%)
Query: 29 ILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88
I+E GA+ + ++ + Y TL++P+ IS S GIT + + + + ++
Sbjct: 31 IIEIGAVKIQGGQI--VDEYHTLIKPSRE--ISRKSSEITGITQEMLENKRSIEEVLPEF 86
Query: 89 FDILHGRIWAGHNILRFDCARIREAFAEI-GRPAPEPKGTIDSLALLTQRFGRRAGDMKM 147
L I HN FD +R ++ G P ID+LAL R+ +
Sbjct: 87 LGFLEDSIIVAHNA-NFDYRFLRLWIKKVMGLDWERP--YIDTLALAKSLLKLRS--YSL 141
Query: 148 ASLATYFGLGQ-QTHRSLDDVRMNLEVL 174
S+ GLG + HR+LDD R+ +V
Sbjct: 142 DSVVEKLGLGPFRHHRALDDARVTAQVF 169
>pdb|1ZBU|A Chain A, Crystal Structure Of Full-Length 3'-Exonuclease
pdb|1ZBU|B Chain B, Crystal Structure Of Full-Length 3'-Exonuclease
pdb|1ZBU|C Chain C, Crystal Structure Of Full-Length 3'-Exonuclease
pdb|1ZBU|D Chain D, Crystal Structure Of Full-Length 3'-Exonuclease
Length = 349
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 33/84 (39%), Gaps = 2/84 (2%)
Query: 10 IAFFDVETTVPTRPGQRFA--ILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRC 67
I D E T F I+EF +L+ LE + VRP +S +
Sbjct: 130 ICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISL 189
Query: 68 NGITPDAVVSSPTFADIADTVFDI 91
GIT D V + TF + V D+
Sbjct: 190 TGITQDQVDRADTFPQVLKKVIDL 213
>pdb|1WLJ|A Chain A, Human Isg20
Length = 189
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 48 YSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDC 107
Y +RP I+ R +G+TP +V + FA + +L G++ GH+ L+ D
Sbjct: 39 YDKFIRPEGE--ITDYRTRVSGVTPQHMVGATPFAVARLEILQLLKGKLVVGHD-LKHDF 95
Query: 108 ARIRE 112
++E
Sbjct: 96 QALKE 100
>pdb|1W0H|A Chain A, Crystallographic Structure Of The Nuclease Domain Of
3'hexo, A Deddh Family Member, Bound To Ramp
Length = 204
Score = 32.3 bits (72), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 32/83 (38%), Gaps = 2/83 (2%)
Query: 10 IAFFDVETTVPTRPGQRFA--ILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRC 67
I D E T F I+EF +L+ LE + VRP +S +
Sbjct: 12 ICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISL 71
Query: 68 NGITPDAVVSSPTFADIADTVFD 90
GIT D V + TF + V D
Sbjct: 72 TGITQDQVDRADTFPQVLKKVID 94
>pdb|4HXH|B Chain B, Structure Of Mrna Stem-loop, Human Stem-loop Binding
Protein And 3'hexo Ternary Complex
pdb|4HXH|E Chain E, Structure Of Mrna Stem-loop, Human Stem-loop Binding
Protein And 3'hexo Ternary Complex
Length = 303
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 32/83 (38%), Gaps = 2/83 (2%)
Query: 10 IAFFDVETTVPTRPGQRFA--ILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRC 67
I D E T F I+EF +L+ LE + VRP +S +
Sbjct: 76 ICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISL 135
Query: 68 NGITPDAVVSSPTFADIADTVFD 90
GIT D V + TF + V D
Sbjct: 136 TGITQDQVDRADTFPQVLKKVID 158
>pdb|3L8C|A Chain A, Structure Of Probable D-Alanine--Poly(Phosphoribitol)
Ligase Subunit-1 From Streptococcus Pyogenes
pdb|3L8C|B Chain B, Structure Of Probable D-Alanine--Poly(Phosphoribitol)
Ligase Subunit-1 From Streptococcus Pyogenes
pdb|3LGX|A Chain A, Structure Of Probable D-Alanine-Poly(Phosphoribitol)
Ligase Subunit-1 From Streptococcus Pyogenes With Atp
pdb|3LGX|B Chain B, Structure Of Probable D-Alanine-Poly(Phosphoribitol)
Ligase Subunit-1 From Streptococcus Pyogenes With Atp
pdb|3LGX|C Chain C, Structure Of Probable D-Alanine-Poly(Phosphoribitol)
Ligase Subunit-1 From Streptococcus Pyogenes With Atp
pdb|3LGX|D Chain D, Structure Of Probable D-Alanine-Poly(Phosphoribitol)
Ligase Subunit-1 From Streptococcus Pyogenes With Atp
Length = 521
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 105 FDCARIREAFAEIGRPAPEPKGTIDSLALLTQR----FGRRAGDMKMASLATYFGLGQQT 160
+DC R + ++ R + IDSLALL + FG + DM LAT+ L +
Sbjct: 23 YDCLGERRTYGQLKRDSDSIAAFIDSLALLAKSPVLVFGAQTYDM----LATFVALTKSG 78
Query: 161 H 161
H
Sbjct: 79 H 79
>pdb|3EMP|A Chain A, Crystal Structure Of The S-Acetanilide Modified Form Of
C165s Ahpc
pdb|3EMP|B Chain B, Crystal Structure Of The S-Acetanilide Modified Form Of
C165s Ahpc
pdb|3EMP|C Chain C, Crystal Structure Of The S-Acetanilide Modified Form Of
C165s Ahpc
pdb|3EMP|D Chain D, Crystal Structure Of The S-Acetanilide Modified Form Of
C165s Ahpc
pdb|3EMP|E Chain E, Crystal Structure Of The S-Acetanilide Modified Form Of
C165s Ahpc
Length = 186
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 24/112 (21%), Positives = 46/112 (41%), Gaps = 10/112 (8%)
Query: 36 LVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGR 95
VCP +L ++ ++ E + L V ++ D + + ++T+ I +
Sbjct: 44 FVCPTELGDVADHY--------EELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAM 95
Query: 96 IW--AGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDM 145
I G FD R E A+ +P+G I ++ + + GR A D+
Sbjct: 96 IGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDL 147
>pdb|1YEP|A Chain A, Structural And Biochemical Analysis Of The Link Between
Enzymatic Activity And Olgomerization In Ahpc, A
Bacterial Peroxiredoxin.
pdb|1YEP|B Chain B, Structural And Biochemical Analysis Of The Link Between
Enzymatic Activity And Olgomerization In Ahpc, A
Bacterial Peroxiredoxin.
pdb|1YEP|C Chain C, Structural And Biochemical Analysis Of The Link Between
Enzymatic Activity And Olgomerization In Ahpc, A
Bacterial Peroxiredoxin.
pdb|1YEP|D Chain D, Structural And Biochemical Analysis Of The Link Between
Enzymatic Activity And Olgomerization In Ahpc, A
Bacterial Peroxiredoxin.
pdb|1YEP|E Chain E, Structural And Biochemical Analysis Of The Link Between
Enzymatic Activity And Olgomerization In Ahpc, A
Bacterial Peroxiredoxin
Length = 186
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 24/112 (21%), Positives = 46/112 (41%), Gaps = 10/112 (8%)
Query: 36 LVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGR 95
VCP +L ++ ++ E + L V ++ D + + ++T+ I +
Sbjct: 44 FVCPTELGDVADHY--------EELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAM 95
Query: 96 IW--AGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDM 145
I G FD R E A+ +P+G I ++ + + GR A D+
Sbjct: 96 IGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDL 147
>pdb|4DAG|H Chain H, Structure Of The Human Metapneumovirus Fusion Protein With
Neutralizing Antibody Identifies A Pneumovirus Antigenic
Site
Length = 220
Score = 28.9 bits (63), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 161 HRSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWVSPNATTRSRSNAK 210
H ++ +R+ + YCA VL S +PD F + W T S ++ K
Sbjct: 79 HLQMNSLRVEDTAIYYCARVLSRASGMPDAFDI--WGPGTMVTVSSASTK 126
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 0.133 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,546,425
Number of Sequences: 62578
Number of extensions: 558637
Number of successful extensions: 1206
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1199
Number of HSP's gapped (non-prelim): 14
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
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: 54 (25.4 bits)