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= 045843
(913 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 577 LKALFLNNCCQLMRLPAEVGDLHNLEILDLSHTGICCLPSEI 618
L L+LN L LPAE+ +L NL +LDLSH + LP+E+
Sbjct: 249 LTRLYLNGNS-LTELPAEIKNLSNLRVLDLSHNRLTSLPAEL 289
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 37.7 bits (86), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 134 RKQIGQIAIMVEKAPVPVIKKH-AKKMEEVPSLNKHLKMLQECLRNVGTKRICIWGPPGV 192
+++I ++A A P ++K+ K ++EV + + + +L++ L++ + +GPPG
Sbjct: 10 KRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGT 69
Query: 193 GKTTIM 198
GKT+ +
Sbjct: 70 GKTSTI 75
>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
Length = 543
Score = 36.6 bits (83), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 172 LQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIGESRQFDFIFWVTVNSEGNIR 226
+Q+ +++ +C+ GPPGVGKT++ +++ ++G R+F I V E IR
Sbjct: 99 VQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLG--RKFVRISLGGVRDESEIR 151
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 36.6 bits (83), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 34/135 (25%), Positives = 58/135 (42%), Gaps = 36/135 (26%)
Query: 778 LETLILKRCHGMKTLFSEEIIFQLNQIQYLQVEDCKEMEEIIEAGSAVDS---------- 827
LETL L R + ++ L + I LN+++ L + C E+ E+ E ++ D+
Sbjct: 129 LETLTLAR-NPLRALPAS--IASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNL 185
Query: 828 ----------RAFP-------KLKSFQLINLP--KLSSICHNMSLAWPLLETITIKACDE 868
R+ P LKS ++ N P L H++ P LE + ++ C
Sbjct: 186 QSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHL----PKLEELDLRGCTA 241
Query: 869 LRNFPSTIENASKLR 883
LRN+P + L+
Sbjct: 242 LRNYPPIFGGRAPLK 256
>pdb|2EWV|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
Bound Adp
Length = 372
Score = 35.8 bits (81), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 63/149 (42%), Gaps = 28/149 (18%)
Query: 161 EVPSLNK---HLKMLQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIGESRQFDFIFWV 217
E+P K K+L+ C R +G I + GP G GK+T + ++ D I +++ + I
Sbjct: 115 EIPEFKKLGLPDKVLELCHRKMGL--ILVTGPTGSGKSTTIASMIDYINQTKSYHII--- 169
Query: 218 TVNSEGNIRDIQEVLLKR----LDLRAEDHNIDQRADMISEELKDKSYVLFLDEV----S 269
I D E + K ++ R + AD + L++ V+F+ E+ +
Sbjct: 170 ------TIEDPIEYVFKHKKSIVNQREVGEDTKSFADALRAALREDPDVIFVGEMRDLET 223
Query: 270 TEINLRDIGIHDEHKNGKVVFACIFRNIC 298
E LR + G +VF + N
Sbjct: 224 VETALR------AAETGHLVFGTLHTNTA 246
>pdb|1G4A|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4A|F Chain F, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|F Chain F, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|K Chain K, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|L Chain L, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1YYF|A Chain A, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
pdb|1YYF|B Chain B, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
Length = 443
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 167 KHLKMLQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIG------ESRQFDFIFWVTVN 220
+ +++ +E V K I + GP GVGKT I L E+ +F + +V
Sbjct: 36 RRMQLNEELRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE 95
Query: 221 SEGNIRDIQEVLLKRLDLRAEDHNIDQRADMISEE 255
+ IRD+ + +K + ++A + N RA+ ++EE
Sbjct: 96 VDSIIRDLTDAAVKMVRVQAIEKN-RYRAEELAEE 129
>pdb|1DO2|A Chain A, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|B Chain B, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|C Chain C, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|D Chain D, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO0|A Chain A, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|B Chain B, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|C Chain C, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|D Chain D, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|E Chain E, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|F Chain F, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
Length = 442
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 167 KHLKMLQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIG------ESRQFDFIFWVTVN 220
+ +++ +E V K I + GP GVGKT I L E+ +F + +V
Sbjct: 35 RRMQLNEELRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE 94
Query: 221 SEGNIRDIQEVLLKRLDLRAEDHNIDQRADMISEE 255
+ IRD+ + +K + ++A + N RA+ ++EE
Sbjct: 95 VDSIIRDLTDAAVKMVRVQAIEKN-RYRAEELAEE 128
>pdb|1E94|E Chain E, Hslv-Hslu From E.Coli
pdb|1E94|F Chain F, Hslv-Hslu From E.Coli
pdb|1HT2|E Chain E, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|F Chain F, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|G Chain G, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|H Chain H, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT1|E Chain E, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|F Chain F, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|G Chain G, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|I Chain I, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HQY|E Chain E, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HQY|F Chain F, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
Length = 449
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 167 KHLKMLQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIG------ESRQFDFIFWVTVN 220
+ +++ +E V K I + GP GVGKT I L E+ +F + +V
Sbjct: 42 RRMQLNEELRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE 101
Query: 221 SEGNIRDIQEVLLKRLDLRAEDHNIDQRADMISEE 255
+ IRD+ + +K + ++A + N RA+ ++EE
Sbjct: 102 VDSIIRDLTDAAVKMVRVQAIEKN-RYRAEELAEE 135
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 33.1 bits (74), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 58/148 (39%), Gaps = 19/148 (12%)
Query: 332 DIKPVARLIINECGGMPHMIKLIGSSLANVSNPAIWRDMLSQLRSPSM-----APKQELE 386
D+ A II EC G P ++ LIG+ L + P W L QL++ + + E
Sbjct: 311 DLPEQAHSIIKECKGSPLVVSLIGALLRDF--PNRWEYYLKQLQNKQFKRIRKSSSYDYE 368
Query: 387 EVYKSFKLVCDKLPSDKQLCLLYWAIFPVGYELHEDYIIECWRAEQFFACLRKLGEARDR 446
+ ++ + + L D + +I ++ + W E +
Sbjct: 369 ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMET------------EE 416
Query: 447 GQSILDEFVKKSLLEKGRKASHYKMFEH 474
+ IL EFV KSLL R ++ + H
Sbjct: 417 VEDILQEFVNKSLLFCDRNGKSFRYYLH 444
>pdb|1G3I|A Chain A, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|B Chain B, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|C Chain C, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|D Chain D, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|E Chain E, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|F Chain F, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|S Chain S, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|T Chain T, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|U Chain U, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|V Chain V, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|W Chain W, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|X Chain X, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G41|A Chain A, Crystal Structure Of Hslu Haemophilus Influenzae
pdb|1KYI|A Chain A, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|B Chain B, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|C Chain C, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|D Chain D, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|E Chain E, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|F Chain F, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|S Chain S, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|T Chain T, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|U Chain U, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|V Chain V, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|W Chain W, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|X Chain X, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
Length = 444
Score = 33.1 bits (74), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 156 AKKMEEVPSLNKHLKM-LQECLRN-VGTKRICIWGPPGVGKTTIMENLHDAIG------E 207
AK+ + N+ +M LQE LR+ V K I + GP GVGKT I L E
Sbjct: 23 AKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVE 82
Query: 208 SRQFDFIFWVTVNSEGNIRDIQEVLLK 234
+ +F + +V + IRD+ + +K
Sbjct: 83 ATKFTEVGYVGKEVDSIIRDLTDSAMK 109
>pdb|3QMZ|A Chain A, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
pdb|3QMZ|B Chain B, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
Length = 2486
Score = 33.1 bits (74), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 10/53 (18%)
Query: 162 VPSLN--KHLKMLQECLRNVGTKRICIWGPPGVGKTTIMEN------LHDAIG 206
+P+++ KH K+ + L + + I + GPPG GKT IM N L+D +G
Sbjct: 1029 IPTIDTIKHEKIFYDLLNS--KRGIILCGPPGSGKTMIMNNALRNSSLYDVVG 1079
>pdb|2GSZ|A Chain A, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|B Chain B, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|C Chain C, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|D Chain D, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|E Chain E, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|F Chain F, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
Length = 363
Score = 33.1 bits (74), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 60/149 (40%), Gaps = 28/149 (18%)
Query: 161 EVPSLNK---HLKMLQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIGESRQFDFIFWV 217
E+P K K+L+ C R G I + GP G GK+T + + D I +++ + I
Sbjct: 104 EIPEFKKLGLPDKVLELCHRKXGL--ILVTGPTGSGKSTTIASXIDYINQTKSYHII--- 158
Query: 218 TVNSEGNIRDIQEVLLKR----LDLRAEDHNIDQRADMISEELKDKSYVLFLDEV----S 269
I D E + K ++ R + AD + L++ V+F+ E +
Sbjct: 159 ------TIEDPIEYVFKHKKSIVNQREVGEDTKSFADALRAALREDPDVIFVGEXRDLET 212
Query: 270 TEINLRDIGIHDEHKNGKVVFACIFRNIC 298
E LR + G +VF + N
Sbjct: 213 VETALR------AAETGHLVFGTLHTNTA 235
>pdb|4AI6|A Chain A, Dynein Motor Domain - Adp Complex
pdb|4AI6|B Chain B, Dynein Motor Domain - Adp Complex
pdb|4AKG|A Chain A, Dynein Motor Domain - Atp Complex
pdb|4AKG|B Chain B, Dynein Motor Domain - Atp Complex
pdb|4AKH|A Chain A, Dynein Motor Domain - Amppnp Complex
pdb|4AKH|B Chain B, Dynein Motor Domain - Amppnp Complex
pdb|4AKI|A Chain A, Dynein Motor Domain - Luac Derivative
pdb|4AKI|B Chain B, Dynein Motor Domain - Luac Derivative
Length = 2695
Score = 33.1 bits (74), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 10/53 (18%)
Query: 162 VPSLN--KHLKMLQECLRNVGTKRICIWGPPGVGKTTIMEN------LHDAIG 206
+P+++ KH K+ + L + + I + GPPG GKT IM N L+D +G
Sbjct: 1248 IPTIDTIKHEKIFYDLLNS--KRGIILCGPPGSGKTMIMNNALRNSSLYDVVG 1298
>pdb|2EWW|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
Bound Atp
Length = 372
Score = 33.1 bits (74), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 60/149 (40%), Gaps = 28/149 (18%)
Query: 161 EVPSLNK---HLKMLQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIGESRQFDFIFWV 217
E+P K K+L+ C R G I + GP G GK+T + + D I +++ + I
Sbjct: 115 EIPEFKKLGLPDKVLELCHRKXGL--ILVTGPTGSGKSTTIASXIDYINQTKSYHII--- 169
Query: 218 TVNSEGNIRDIQEVLLKR----LDLRAEDHNIDQRADMISEELKDKSYVLFLDEV----S 269
I D E + K ++ R + AD + L++ V+F+ E +
Sbjct: 170 ------TIEDPIEYVFKHKKSIVNQREVGEDTKSFADALRAALREDPDVIFVGEXRDLET 223
Query: 270 TEINLRDIGIHDEHKNGKVVFACIFRNIC 298
E LR + G +VF + N
Sbjct: 224 VETALR------AAETGHLVFGTLHTNTA 246
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 32.7 bits (73), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 142 IMVEKAP------VPVIKKHAKKMEEVPSLNKHLKMLQECLRNVGTKRICIWGPPGVGKT 195
+MVEK P V + K K+++EV L L E L K + ++GPPG GKT
Sbjct: 137 MMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKT 196
>pdb|2EYU|A Chain A, The Crystal Structure Of The C-Terminal Domain Of Aquifex
Aeolicus Pilt
pdb|2EYU|B Chain B, The Crystal Structure Of The C-Terminal Domain Of Aquifex
Aeolicus Pilt
Length = 261
Score = 32.7 bits (73), Expect = 1.0, Method: Composition-based stats.
Identities = 36/147 (24%), Positives = 60/147 (40%), Gaps = 28/147 (19%)
Query: 161 EVPSLNK---HLKMLQECLRNVGTKRICIWGPPGVGKTTIMENLHDAIGESRQFDFIFWV 217
E+P K K+L+ C R G I + GP G GK+T + + D I +++ + I
Sbjct: 4 EIPEFKKLGLPDKVLELCHRKXGL--ILVTGPTGSGKSTTIASXIDYINQTKSYHII--- 58
Query: 218 TVNSEGNIRDIQEVLLKR----LDLRAEDHNIDQRADMISEELKDKSYVLFLDEV----S 269
I D E + K ++ R + AD + L++ V+F+ E +
Sbjct: 59 ------TIEDPIEYVFKHKKSIVNQREVGEDTKSFADALRAALREDPDVIFVGEXRDLET 112
Query: 270 TEINLRDIGIHDEHKNGKVVFACIFRN 296
E LR + G +VF + N
Sbjct: 113 VETALR------AAETGHLVFGTLHTN 133
>pdb|3A9R|A Chain A, X-Ray Structures Of Bacillus Pallidus D-Arabinose
Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
pdb|3A9R|B Chain B, X-Ray Structures Of Bacillus Pallidus D-Arabinose
Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
pdb|3A9R|C Chain C, X-Ray Structures Of Bacillus Pallidus D-Arabinose
Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
pdb|3A9S|A Chain A, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With Glycerol
pdb|3A9S|B Chain B, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With Glycerol
pdb|3A9S|C Chain C, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With Glycerol
pdb|3A9T|A Chain A, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With L-Fucitol
pdb|3A9T|B Chain B, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With L-Fucitol
pdb|3A9T|C Chain C, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With L-Fucitol
Length = 595
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 10/43 (23%)
Query: 626 YFPNVGLLQNFINASKSWNG----------NSNFRSFSILVGY 658
YFPN ++ +N+S WNG N N S+L GY
Sbjct: 313 YFPNGDFMETILNSSFDWNGKRAPYIFATENDNLNGISMLFGY 355
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 184 ICIWGPPGVGKTTIME 199
+ +WGPPG GKTT+ E
Sbjct: 53 MILWGPPGTGKTTLAE 68
>pdb|1OFH|A Chain A, Asymmetric Complex Between Hslv And I-domain Deleted Hslu
(h. Influenzae)
pdb|1OFH|B Chain B, Asymmetric Complex Between Hslv And I-domain Deleted Hslu
(h. Influenzae)
pdb|1OFH|C Chain C, Asymmetric Complex Between Hslv And I-domain Deleted Hslu
(h. Influenzae)
pdb|1OFI|A Chain A, Asymmetric Complex Between Hslv And I-Domain Deleted Hslu
(H. Influenzae)
pdb|1OFI|B Chain B, Asymmetric Complex Between Hslv And I-Domain Deleted Hslu
(H. Influenzae)
pdb|1OFI|C Chain C, Asymmetric Complex Between Hslv And I-Domain Deleted Hslu
(H. Influenzae)
Length = 310
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 156 AKKMEEVPSLNKHLKM-LQECLRN-VGTKRICIWGPPGVGKTTIMENLHDAIG------E 207
AK+ + N+ +M LQE LR+ V K I + GP GVGKT I L E
Sbjct: 23 AKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVE 82
Query: 208 SRQFDFIFWVTVNSEGNIRDIQE 230
+ +F + +V + IRD+ +
Sbjct: 83 ATKFTEVGYVGKEVDSIIRDLTD 105
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 58/148 (39%), Gaps = 19/148 (12%)
Query: 332 DIKPVARLIINECGGMPHMIKLIGSSLANVSNPAIWRDMLSQLRSPSM-----APKQELE 386
D+ A II EC G P ++ LIG+ L + P W L QL++ + + E
Sbjct: 305 DLPEQAHSIIKECKGSPLVVSLIGALLRDF--PNRWEYYLKQLQNKQFKRIRKSSSYDYE 362
Query: 387 EVYKSFKLVCDKLPSDKQLCLLYWAIFPVGYELHEDYIIECWRAEQFFACLRKLGEARDR 446
+ ++ + + L D + +I ++ + W E +
Sbjct: 363 ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMET------------EE 410
Query: 447 GQSILDEFVKKSLLEKGRKASHYKMFEH 474
+ IL EFV KSLL R ++ + H
Sbjct: 411 VEDILQEFVNKSLLFCDRNGKSFRYYLH 438
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 73/320 (22%), Positives = 126/320 (39%), Gaps = 60/320 (18%)
Query: 184 ICIWGPPGVGKTTIM-ENLHD-AIGESRQFDFIFWVTVNSE---GNIRDIQEVLLKRLDL 238
+ I+G G GK+ + E + D ++ E + WV++ + G + +Q + + RLD
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCM-RLD- 207
Query: 239 RAEDHNIDQRADMISEELKDKSYVLFLDEVSTEINLRDIGIHDEHKNGKVVFACIFRNIC 298
++ + QR + EE KD+ VL L + + R + I D+ + V+ A F N C
Sbjct: 208 --QEESFSQRLPLNIEEAKDRLRVLMLRK-----HPRSLLILDDVWDPWVLKA--FDNQC 258
Query: 299 G-------------------QIDEEVNVQRLSGKDAQKLFWETVGVQLKDCRDIKPVARL 339
+ E + R G + LF V +K D+ A
Sbjct: 259 QILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLF-----VNMKK-EDLPAEAHS 312
Query: 340 IINECGGMPHMIKLIGSSLANVSNPAIWRDMLSQLRSPSM-----APKQELEEVYKSFKL 394
II EC G P ++ LIG+ L + P W L QL++ + + E + ++ +
Sbjct: 313 IIKECKGSPLVVSLIGALLRDF--PNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSI 370
Query: 395 VCDKLPSDKQLCLLYWAIFPVGYELHEDYIIECWRAEQFFACLRKLGEARDRGQSILDEF 454
+ L D + +I ++ + W E + + IL EF
Sbjct: 371 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLET------------EEVEDILQEF 418
Query: 455 VKKSLLEKGRKASHYKMFEH 474
V KSLL R + + H
Sbjct: 419 VNKSLLFCNRNGKSFCYYLH 438
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 73/320 (22%), Positives = 126/320 (39%), Gaps = 60/320 (18%)
Query: 184 ICIWGPPGVGKTTIM-ENLHD-AIGESRQFDFIFWVTVNSE---GNIRDIQEVLLKRLDL 238
+ I+G G GK+ + E + D ++ E + WV++ + G + +Q + + RLD
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCM-RLD- 214
Query: 239 RAEDHNIDQRADMISEELKDKSYVLFLDEVSTEINLRDIGIHDEHKNGKVVFACIFRNIC 298
++ + QR + EE KD+ VL L + + R + I D+ + V+ A F N C
Sbjct: 215 --QEESFSQRLPLNIEEAKDRLRVLMLRK-----HPRSLLILDDVWDPWVLKA--FDNQC 265
Query: 299 G-------------------QIDEEVNVQRLSGKDAQKLFWETVGVQLKDCRDIKPVARL 339
+ E + R G + LF V +K D+ A
Sbjct: 266 QILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLF-----VNMKK-EDLPAEAHS 319
Query: 340 IINECGGMPHMIKLIGSSLANVSNPAIWRDMLSQLRSPSM-----APKQELEEVYKSFKL 394
II EC G P ++ LIG+ L + P W L QL++ + + E + ++ +
Sbjct: 320 IIKECKGSPLVVSLIGALLRDF--PNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSI 377
Query: 395 VCDKLPSDKQLCLLYWAIFPVGYELHEDYIIECWRAEQFFACLRKLGEARDRGQSILDEF 454
+ L D + +I ++ + W E + + IL EF
Sbjct: 378 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLET------------EEVEDILQEF 425
Query: 455 VKKSLLEKGRKASHYKMFEH 474
V KSLL R + + H
Sbjct: 426 VNKSLLFCNRNGKSFCYYLH 445
>pdb|1XZP|A Chain A, Structure Of The Gtp-Binding Protein Trme From Thermotoga
Maritima
pdb|1XZQ|A Chain A, Structure Of The Gtp-binding Protein Trme From Thermotoga
Maritima Complexed With 5-formyl-thf
Length = 482
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 65/134 (48%), Gaps = 21/134 (15%)
Query: 183 RICIWGPPGVGKTTIMENLHDAIGESRQFDFIFWVTVNSEGNIRD-------IQEVLLKR 235
R+ I G P VGK+T++ L + E R + + G RD I+ +L +
Sbjct: 245 RMVIVGKPNVGKSTLLNRL---LNEDRA------IVTDIPGTTRDVISEEIVIRGILFRI 295
Query: 236 LD---LRAEDHNIDQR--ADMISEELKDKSYVLFLDEVSTEINLRDIGIHDEHKNGKVVF 290
+D +R+E +++ +R + +E++ VLF+ + S+ ++ D I + KN + +
Sbjct: 296 VDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLV 355
Query: 291 ACIFRNICGQIDEE 304
++ +I+EE
Sbjct: 356 VINKVDVVEKINEE 369
>pdb|1IM2|A Chain A, Hslu, Haemophilus Influenzae, Selenomethionine Variant
Length = 444
Score = 30.8 bits (68), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 171 MLQECLRN-VGTKRICIWGPPGVGKTTIMENLHDAIG------ESRQFDFIFWVTVNSEG 223
LQE LR+ V K I GP GVGKT I L E+ +F + +V +
Sbjct: 39 QLQEPLRHEVTPKNILXIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDS 98
Query: 224 NIRDIQEVLLK 234
IRD+ + K
Sbjct: 99 IIRDLTDSAXK 109
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 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,228,783
Number of Sequences: 62578
Number of extensions: 1023111
Number of successful extensions: 2532
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 2509
Number of HSP's gapped (non-prelim): 49
length of query: 913
length of database: 14,973,337
effective HSP length: 108
effective length of query: 805
effective length of database: 8,214,913
effective search space: 6613004965
effective search space used: 6613004965
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: 56 (26.2 bits)