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= 016398
(390 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PXZ|A Chain A, 1.7 Angstrom Crystal Structure Of Jun A 1, The Major
Allergen From Cedar Pollen
pdb|1PXZ|B Chain B, 1.7 Angstrom Crystal Structure Of Jun A 1, The Major
Allergen From Cedar Pollen
Length = 346
Score = 317 bits (813), Expect = 6e-87, Method: Compositional matrix adjust.
Identities = 156/314 (49%), Positives = 206/314 (65%), Gaps = 4/314 (1%)
Query: 41 NPIDDCWRCDSEWESNRKALADCAVGFGRNAVGGRDGEIYIVKSKDDDPVDPIPGSLRYA 100
NPID CWR DS W+ NR LADCAVGFG + +GG+ G+ Y V S DD+PV+P PG+LRY
Sbjct: 2 NPIDSCWRGDSNWDQNRMKLADCAVGFGSSTMGGKGGDFYTVTSTDDNPVNPTPGTLRYG 61
Query: 101 VIQEEPLWIIFDHDMVINLKQELVMNSYKTIDGRGFNVQMSNG-PCISIYNVSNIIIHNI 159
+E+ LWIIF +M I LK L + +KTIDGRG +V + NG PC+ + VS++I+H++
Sbjct: 62 ATREKALWIIFSQNMNIKLKMPLYVAGHKTIDGRGADVHLGNGGPCLFMRKVSHVILHSL 121
Query: 160 YIHDCVPA--GSAVVRDSPKHYGPRGRSDGDGISIFGSRDIWIDHCTFSHCYDGLIDIVY 217
+IH C + G +V +S P DGD I++ + WIDH + S C DGLID+
Sbjct: 122 HIHGCNTSVLGDVLVSESIG-VEPVHAQDGDAITMRNVTNAWIDHNSLSDCSDGLIDVTL 180
Query: 218 GSTAITISNNYMFHHNEVMLMGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHI 277
GST ITISNN+ F+H++VML+GH D + DK+M+VT+AFN FG QRMPR R+G H+
Sbjct: 181 GSTGITISNNHFFNHHKVMLLGHDDTYDDDKSMKVTVAFNQFGPNAGQRMPRARYGLVHV 240
Query: 278 VNNIYTGWEMYAIGGSANPTINSQGNVFIASNDESTKEVTKHEIISEDDEWKKWNWRSEG 337
NN Y W +YAIGGS+NPTI S+GN F A ++ KEVTK W WRS
Sbjct: 241 ANNNYDPWNIYAIGGSSNPTILSEGNSFTAPSESYKKEVTKRIGCESPSACANWVWRSTR 300
Query: 338 DLMLNGAFFTPSGQ 351
D +NGA+F SG+
Sbjct: 301 DAFINGAYFVSSGK 314
>pdb|3ZSC|A Chain A, Catalytic Function And Substrate Recognition Of The
Pectate Lyase From Thermotoga Maritima
Length = 340
Score = 94.7 bits (234), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 86/271 (31%), Positives = 124/271 (45%), Gaps = 45/271 (16%)
Query: 59 ALADCAVGFG--------RNAVGGRDGEIYIVKSKDDDPVDPIPGSLRYAVIQEEPLWII 110
+L D VGF VGG GEI V++ ++ L E I+
Sbjct: 1 SLNDKPVGFASVPTADLPEGTVGGLGGEIVFVRTAEE---------LEKYTTAEGKYVIV 51
Query: 111 FDHDMVINLKQELVMNSYKTIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSA 170
D +V K+E+ + S KTI G N G + I + N+II NI+ G
Sbjct: 52 VDGTIVFEPKREIKVLSDKTI--VGINDAKIVGGGLVIKDAQNVIIRNIHFE-----GFY 104
Query: 171 VVRDSPKHYGPRGRS-DGDGISIFGSRDIWIDHCTFSHCYDGLIDIVYGSTAITISNNYM 229
+ D PRG+ D D I++ S IWIDH TF + DG +DI S IT+S N
Sbjct: 105 MEDD------PRGKKYDFDYINVENSHHIWIDHITFVNGNDGAVDIKKYSNYITVSWNKF 158
Query: 230 FHHNEVMLMGHSDD---FSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIY---- 282
H++V L+G SD A + +VT N+F + L+QRMPR R G H+ NN Y
Sbjct: 159 VDHDKVSLVGSSDKEDPEQAGQAYKVTYHHNYFKN-LIQRMPRIRFGMAHVFNNFYSMGL 217
Query: 283 -TG-----WEMYAIGGSANPTINSQGNVFIA 307
TG + +Y + + ++ +GN F+
Sbjct: 218 RTGVSGNVFPIYGVASAMGAKVHVEGNYFMG 248
>pdb|1PCL|A Chain A, Unusual Structural Features In The Parallel Beta-Helix In
Pectate Lyases
Length = 355
Score = 82.0 bits (201), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 76/272 (27%), Positives = 119/272 (43%), Gaps = 53/272 (19%)
Query: 69 RNAVGGRDGEIYIVKSKDDDPVDPIPGSLRYAVIQEEPLWIIFDHDMVINLKQELVMNSY 128
+ A+ G D I+K P+D I G Y ++ + ++ + S
Sbjct: 37 KKALNGTDSSAKIIKVTG--PID-ISGGKAYTSFDDQKA------------RSQISIPSN 81
Query: 129 KTIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHY--GPRGRSD 186
TI G G N + +NG + I V N+I+ N+YI V D HY G ++
Sbjct: 82 TTIIGVGSNGKFTNGSLV-IKGVKNVILRNLYIETPV--------DVAPHYESGDGWNAE 132
Query: 187 GDGISIFGSRDIWIDHCTFSHC-----------------YDGLIDIVYGSTAITISNNYM 229
D I S ++W+DH T S +DG +DI GS +TIS +
Sbjct: 133 WDAAVIDNSTNVWVDHVTISDGSFTDDKYTTKDGEKYVQHDGALDIKKGSDYVTISYSRF 192
Query: 230 FHHNEVMLMGHSDDFSADKNMQVTIAF--NFFGDGLVQRMPRCRHGFFHIVNNIYTG--- 284
H++ +L+GHSD + + ++ + F N F D + +R PR R G H NN+Y G
Sbjct: 193 ELHDKTILIGHSDSNGSQDSGKLRVTFHNNVF-DRVTERAPRVRFGSIHAYNNVYLGDVK 251
Query: 285 ----WEMYAIGGSANPTINSQGNVFIASNDES 312
+Y+ G + +I S+ N F SN +S
Sbjct: 252 HSVYPYLYSFGLGTSGSILSESNSFTLSNLKS 283
>pdb|1OOC|A Chain A, Mutations In The T1.5 Loop Of Pectate Lyase A
pdb|1OOC|B Chain B, Mutations In The T1.5 Loop Of Pectate Lyase A
pdb|1PE9|A Chain A, Mutations In The T1.5 Loop Of Pectate Lyase A
pdb|1PE9|B Chain B, Mutations In The T1.5 Loop Of Pectate Lyase A
Length = 361
Score = 77.8 bits (190), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 66/226 (29%), Positives = 109/226 (48%), Gaps = 40/226 (17%)
Query: 120 KQELVMNSYKTIDGRGFNVQMSNGPCI--SIYNVSNIIIHNIYIHDCVPAGSAVVRDSPK 177
+ ++ + + T+ G G + + NG I +N+II N+YI + D
Sbjct: 80 RSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPI--------DVEP 131
Query: 178 HY--GPRGRSDGDGISIF-GSRDIWIDHCTFSHC-----------------YDGLIDIVY 217
HY G ++ D ++I G+ +WIDH T S +DG +DI
Sbjct: 132 HYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKR 191
Query: 218 GSTAITISNNYMFHHNEVMLMGHSD-DFSADK-NMQVTIAFNFFGDGLVQRMPRCRHGFF 275
GS +TISN+ + H++ ML+GHSD + S DK + VT+ N F + + +R PR R+G
Sbjct: 192 GSDYVTISNSLIDQHDKTMLIGHSDSNGSQDKGKLHVTLFNNVF-NRVTERAPRVRYGSI 250
Query: 276 HIVNNIYTG-------WEMYAIGGSANPTINSQGNVFIASNDESTK 314
H NN++ G Y+ G + ++ S+GN F +N ++K
Sbjct: 251 HSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASK 296
>pdb|1JRG|A Chain A, Crystal Structure Of The R3 Form Of Pectate Lyase A,
Erwinia Chrysanthemi
pdb|1JRG|B Chain B, Crystal Structure Of The R3 Form Of Pectate Lyase A,
Erwinia Chrysanthemi
pdb|1JTA|A Chain A, Crystal Structure Of Pectate Lyase A (C2 Form)
Length = 361
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 66/216 (30%), Positives = 104/216 (48%), Gaps = 40/216 (18%)
Query: 130 TIDGRGFNVQMSNGPCI--SIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHY--GPRGRS 185
T+ G G + + NG I +N+II N+YI + D HY G +
Sbjct: 90 TVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPI--------DVEPHYEKGDGWNA 141
Query: 186 DGDGISIF-GSRDIWIDHCTFSHC-----------------YDGLIDIVYGSTAITISNN 227
+ D ++I G+ +WIDH T S +DG +DI GS +TISN+
Sbjct: 142 EWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNS 201
Query: 228 YMFHHNEVMLMGHSDDFSA-DK-NMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIYTG- 284
+ H++ ML+GH+D SA DK + VT+ N F + + +R PR R+G H NN++ G
Sbjct: 202 LIDQHDKTMLIGHNDTNSAQDKGKLHVTLFNNVF-NRVTERAPRVRYGSIHSFNNVFKGD 260
Query: 285 ------WEMYAIGGSANPTINSQGNVFIASNDESTK 314
Y+ G + ++ S+GN F +N ++K
Sbjct: 261 AKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASK 296
>pdb|1VBL|A Chain A, Structure Of The Thermostable Pectate Lyase Pl 47
Length = 416
Score = 74.7 bits (182), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 69/217 (31%), Positives = 98/217 (45%), Gaps = 48/217 (22%)
Query: 123 LVMNSYKTIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPR 182
+ + S +I G G + ++ G + I NV N+II NI ++P Y P
Sbjct: 128 VYVGSNTSIIGVGKDAKIKGGGFL-IKNVDNVIIRNIEF------------EAPLDYFPE 174
Query: 183 G----------RSDGDGISIFGSRDIWIDHCTFS-----------------HCYDGLIDI 215
S+ D ISI GS IWIDH TF+ +DG +DI
Sbjct: 175 WDPTDGTLGEWNSEYDSISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQHDGALDI 234
Query: 216 VYGSTAITISNNYMFHHNEVMLMGHSDDFSADK-NMQVTIAFNFFGDGLVQRMPRCRHGF 274
S ITIS N +H++V L+G SD AD +++VT+ N++ + + QR+PR R G
Sbjct: 235 KNSSDFITISYNVFTNHDKVTLIGASDSRMADSGHLRVTLHHNYYKN-VTQRLPRVRFGQ 293
Query: 275 FHIVNNIYTGWEM------YAIGGSANPTINSQGNVF 305
HI NN Y + YA G I +Q N F
Sbjct: 294 VHIYNNYYEFSNLADYDFQYAWGVGVFSQIYAQNNYF 330
>pdb|3KRG|A Chain A, Structural Insights Into Substrate Specificity And The
Anti Beta-Elimination Mechanism Of Pectate Lyase
Length = 399
Score = 69.3 bits (168), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 63/207 (30%), Positives = 86/207 (41%), Gaps = 42/207 (20%)
Query: 130 TIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDG-- 187
TI G G N ++ G N+II NI D D + P S G
Sbjct: 130 TIVGSGTNAKVVGGNFQ--IKSDNVIIRNIEFQDAY--------DYFPQWDPTAGSSGNW 179
Query: 188 ----DGISIFGSRDIWIDHCTFS-----------------HCYDGLIDIVYGSTAITISN 226
D I+I G IWIDHCTF+ +DG D G+ IT+S
Sbjct: 180 ASQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSY 239
Query: 227 NYMFHHNEVMLMGHSDDFSADK-NMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIYTGW 285
NY H+ + G SD ++D +++T+ N + + +VQR PR R G H+ NN Y G
Sbjct: 240 NYYHDHDASSIFGSSDSKTSDDGKLKITLHHNRYKN-IVQRAPRVRFGQVHVYNNYYEGS 298
Query: 286 EM-------YAIGGSANPTINSQGNVF 305
YA G + I +Q NV
Sbjct: 299 TSSSSYPFSYAWGIGKSSKIYAQNNVI 325
>pdb|1BN8|A Chain A, Bacillus Subtilis Pectate Lyase
Length = 420
Score = 68.9 bits (167), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 63/207 (30%), Positives = 87/207 (42%), Gaps = 42/207 (20%)
Query: 130 TIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDG-- 187
TI G G N ++ G N+II NI D D + P S G
Sbjct: 151 TIVGSGTNAKVVGGNFQ--IKSDNVIIRNIEFQDAY--------DYFPQWDPTDGSSGNW 200
Query: 188 ----DGISIFGSRDIWIDHCTFS-----------------HCYDGLIDIVYGSTAITISN 226
D I+I G IWIDHCTF+ +DG D G+ IT+S
Sbjct: 201 NSQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSY 260
Query: 227 NYMFHHNEVMLMGHSDDFSADK-NMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIYTGW 285
NY H++ + G SD ++D +++T+ N + + +VQR PR R G H+ NN Y G
Sbjct: 261 NYYHDHDKSSIFGSSDSKTSDDGKLKITLHHNRYKN-IVQRAPRVRFGQVHVYNNYYEGS 319
Query: 286 EM-------YAIGGSANPTINSQGNVF 305
YA G + I +Q NV
Sbjct: 320 TSSSSYPFSYAWGIGKSSKIYAQNNVI 346
>pdb|2BSP|A Chain A, Bacillus Subtilis Pectate Lyase R279k Mutant
Length = 420
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 62/207 (29%), Positives = 87/207 (42%), Gaps = 42/207 (20%)
Query: 130 TIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDG-- 187
TI G G N ++ G N+II NI D D + P S G
Sbjct: 151 TIVGSGTNAKVVGGNFQ--IKSDNVIIRNIEFQDAY--------DYFPQWDPTDGSSGNW 200
Query: 188 ----DGISIFGSRDIWIDHCTFS-----------------HCYDGLIDIVYGSTAITISN 226
D I+I G IWIDHCTF+ +DG D G+ IT+S
Sbjct: 201 NSQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSY 260
Query: 227 NYMFHHNEVMLMGHSDDFSADK-NMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIYTGW 285
NY H++ + G SD ++D +++T+ N + + +VQ+ PR R G H+ NN Y G
Sbjct: 261 NYYHDHDKSSIFGSSDSKTSDDGKLKITLHHNRYKN-IVQKAPRVRFGQVHVYNNYYEGS 319
Query: 286 EM-------YAIGGSANPTINSQGNVF 305
YA G + I +Q NV
Sbjct: 320 TSSSSYPFSYAWGIGKSSKIYAQNNVI 346
>pdb|2NZM|A Chain A, Hexasaccharide I Bound To Bacillus Subtilis Pectate Lyase
pdb|2O04|A Chain A, Pectate Lyase Bound To Hexasaccharide Compound Ii
pdb|2O0V|A Chain A, Pectate Lyase Bound To Hexasaccharide Compound Iii
pdb|2O0W|A Chain A, Pectate Lyase Bound To Hexasaccharide Compound Iv
pdb|2O17|A Chain A, Pectate Lyase Bound To Hexasaccharide
pdb|2O1D|A Chain A, Pectate Lyase Bound To Trisaccharide
Length = 399
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 62/207 (29%), Positives = 86/207 (41%), Gaps = 42/207 (20%)
Query: 130 TIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDG-- 187
TI G G N ++ G N+II NI D D + P S G
Sbjct: 130 TIVGSGTNAKVVGGNFQ--IKSDNVIIRNIEFQDAY--------DYFPQWDPTDGSSGNW 179
Query: 188 ----DGISIFGSRDIWIDHCTFS-----------------HCYDGLIDIVYGSTAITISN 226
D I+I G IWIDHCTF+ +DG D G+ IT+S
Sbjct: 180 NSQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSY 239
Query: 227 NYMFHHNEVMLMGHSDDFSADK-NMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIYTGW 285
NY H++ + G SD ++D +++T+ N + + +VQ PR R G H+ NN Y G
Sbjct: 240 NYYHDHDKSSIFGSSDSKTSDDGKLKITLHHNRYKN-IVQAAPRVRFGQVHVYNNYYEGS 298
Query: 286 EM-------YAIGGSANPTINSQGNVF 305
YA G + I +Q NV
Sbjct: 299 TSSSSYPFSYAWGIGKSSKIYAQNNVI 325
>pdb|3VMV|A Chain A, Crystal Structure Of Pectate Lyase Bsp165pela From
Bacillus Sp. N165
pdb|3VMW|A Chain A, Crystal Structure Of Pectate Lyase Bsp165pela From
Bacillus Sp. N165 In Complex With Trigalacturonate
Length = 326
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 54/188 (28%), Positives = 85/188 (45%), Gaps = 35/188 (18%)
Query: 130 TIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDGDG 189
+I G G N + +G I + N NIII N+ IH +G+G
Sbjct: 82 SIIGVGTNGEF-DGIGIRLSNAHNIIIQNVSIHHV--------------------REGEG 120
Query: 190 ISIF---GSRDIWIDHCTF---------SHCYDGLIDIVYGSTAITISNNYMFHHNEVML 237
+I S+++WIDH F S YDGL+D+ + IT+S N +H + ML
Sbjct: 121 TAIEVTDDSKNVWIDHNEFYSEFPGNGDSDYYDGLVDMKRNAEYITVSWNKFENHWKTML 180
Query: 238 MGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIYTGWEMYAIGGSANPT 297
+GH+D+ S + ++T N+F + L R+P R+ H+ NN + AI
Sbjct: 181 VGHTDNASLAPD-KITYHHNYF-NNLNSRVPLIRYADVHMFNNYFKDINDTAINSRVGAR 238
Query: 298 INSQGNVF 305
+ + N F
Sbjct: 239 VFVENNYF 246
>pdb|2QX3|A Chain A, Structure Of Pectate Lyase Ii From Xanthomonas Campestris
Pv. Campestris Str. Atcc 33913
pdb|2QX3|B Chain B, Structure Of Pectate Lyase Ii From Xanthomonas Campestris
Pv. Campestris Str. Atcc 33913
Length = 330
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 73/165 (44%), Gaps = 34/165 (20%)
Query: 134 RGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDGDGISIF 193
+G N +N + N N+II N+ I +G D D IS+
Sbjct: 77 KGANGSAANFGIRVVGNAHNVIIQNMTIGLL-----------------QGGEDADSISLE 119
Query: 194 GSRD-----IWIDHCT----FSHC-------YDGLIDIVYGSTAITISNNYMFHHNEVML 237
G+ IW+DH T + C +DG ID+ G +T+S NY++++ +V L
Sbjct: 120 GNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVAL 179
Query: 238 MGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIY 282
G+SD + + + T N F + + R+P R G HI NN +
Sbjct: 180 NGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRRGLSHIYNNYF 223
>pdb|1PLU|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi With 1 Lu+3 Ion
In The Putative Calcium Binding Site
pdb|1O88|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 11.2 With
30mm Ca2+
pdb|1O8D|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 11.2 With
5mm Ca2+
pdb|1O8E|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 11.2 With
1mm Ca2+
pdb|1O8F|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
30mm Ca2+
pdb|1O8G|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
5mm Ca2+
pdb|1O8H|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
0.3mm Ca2+ Added
pdb|1O8I|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 9.5 With
No Ca2+ Added
pdb|1O8J|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
30mm Ca2+
pdb|1O8K|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
20mm Ca2+
pdb|1O8L|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
5mm Ca2+
pdb|1O8M|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi At Ph 4.5 With
No Ca2+ Added
pdb|1AIR|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi (Ec16) To A
Resolution Of 2.2 Angstroms With 128 Waters
pdb|2PEC|A Chain A, The Refined Three-Dimensional Structure Of Pectate Lyase C
From Erwinia Chrysanthemi At 2.2 Angstroms Resolution:
Implications For An Enzymatic Mechanism
Length = 353
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 41/126 (32%), Positives = 60/126 (47%), Gaps = 17/126 (13%)
Query: 171 VVRDSPKHYGPRGRSDGDGISIFGSRDIWIDHCTF---SHCYDGL----------IDIVY 217
VV++ Y P G DGD I + S ++W+DH +H DG +DI
Sbjct: 114 VVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKG 173
Query: 218 GSTAITISNNYMFHHNEVMLMGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHI 277
S +T+S NY+ +V L G S S+D +T N++ D + R+P R G H
Sbjct: 174 ASNTVTVSYNYIHGVKKVGLDGSS---SSDTGRNITYHHNYYND-VNARLPLQRGGLVHA 229
Query: 278 VNNIYT 283
NN+YT
Sbjct: 230 YNNLYT 235
>pdb|2QXZ|A Chain A, Pectate Lyase R236f From Xanthomonas Campestris
pdb|2QXZ|B Chain B, Pectate Lyase R236f From Xanthomonas Campestris
Length = 330
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 73/165 (44%), Gaps = 34/165 (20%)
Query: 134 RGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDGDGISIF 193
+G N +N + N N+II N+ I +G D D IS+
Sbjct: 77 KGANGSAANFGIRVVGNAHNVIIQNMTIGLL-----------------QGGEDADSISLE 119
Query: 194 GSRD-----IWIDHCT----FSHC-------YDGLIDIVYGSTAITISNNYMFHHNEVML 237
G+ IW+DH T + C +DG ID+ G +T+S NY++++ +V L
Sbjct: 120 GNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVAL 179
Query: 238 MGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIY 282
G+SD + + + T N F + + R+P R G HI NN +
Sbjct: 180 NGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRFGLSHIYNNYF 223
>pdb|2QY1|A Chain A, Pectate Lyase A31g/r236f From Xanthomonas Campestris
pdb|2QY1|B Chain B, Pectate Lyase A31g/r236f From Xanthomonas Campestris
Length = 330
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 73/165 (44%), Gaps = 34/165 (20%)
Query: 134 RGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRGRSDGDGISIF 193
+G N +N + N N+II N+ I +G D D IS+
Sbjct: 77 KGANGSAANFGIRVVGNAHNVIIQNMTIGLL-----------------QGGEDADSISLE 119
Query: 194 GSRD-----IWIDHCT----FSHC-------YDGLIDIVYGSTAITISNNYMFHHNEVML 237
G+ IW+DH T + C +DG ID+ G +T+S NY++++ +V L
Sbjct: 120 GNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVAL 179
Query: 238 MGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHIVNNIY 282
G+SD + + + T N F + + R+P R G HI NN +
Sbjct: 180 NGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRFGLSHIYNNYF 223
>pdb|2EWE|A Chain A, Crystal Structure Of Pectate Lyase C R218k Mutant In
Complex With Pentagalacturonic Acid
Length = 353
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 40/126 (31%), Positives = 60/126 (47%), Gaps = 17/126 (13%)
Query: 171 VVRDSPKHYGPRGRSDGDGISIFGSRDIWIDHCTF---SHCYDGL----------IDIVY 217
VV++ Y P G DGD I + S ++W+DH +H DG +DI
Sbjct: 114 VVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKG 173
Query: 218 GSTAITISNNYMFHHNEVMLMGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCRHGFFHI 277
S +T+S NY+ +V L G S S+D +T N++ D + ++P R G H
Sbjct: 174 ASNTVTVSYNYIHGVKKVGLDGSS---SSDTGRNITYHHNYYND-VNAKLPLQRGGLVHA 229
Query: 278 VNNIYT 283
NN+YT
Sbjct: 230 YNNLYT 235
>pdb|1QCX|A Chain A, Pectin Lyase B
Length = 359
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 52/199 (26%), Positives = 86/199 (43%), Gaps = 42/199 (21%)
Query: 123 LVMNSYKTIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPR 182
+ +NS K+I G+G + + N+II NI + D P+
Sbjct: 104 ITVNSNKSIVGQGTKGVIKGKGLRVVSGAKNVIIQNIAVTDI---------------NPK 148
Query: 183 GRSDGDGISIFGSRDIWIDHCTFSHCYDGLIDIVYGSTA---ITISNNYM---------- 229
GD I++ S +WIDH T + G IV G++A +TIS + +
Sbjct: 149 YVWGGDAITVDDSDLVWIDHVTTARI--GRQHIVLGTSADNRVTISYSLIDGRSDYSATC 206
Query: 230 --FHHNEVMLMGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCR-HGFFHIVNNIYTGWE 286
H+ V L G +D VT+ N+F + L RMP+ + + H VNN++ ++
Sbjct: 207 NGHHYWGVYLDGSND--------MVTLKGNYFYN-LSGRMPKVQGNTLLHAVNNLFHNFD 257
Query: 287 MYAIGGSANPTINSQGNVF 305
+A + ++GNVF
Sbjct: 258 GHAFEIGTGGYVLAEGNVF 276
>pdb|1IDK|A Chain A, Pectin Lyase A
Length = 359
Score = 32.0 bits (71), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 45/199 (22%), Positives = 79/199 (39%), Gaps = 42/199 (21%)
Query: 123 LVMNSYKTIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPR 182
+ + S K++ G G + + + NIII NI + D P+
Sbjct: 104 ITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDI---------------NPK 148
Query: 183 GRSDGDGISIFGSRDIWIDHCTFSHCYDGLIDIVYGSTA---ITISNNYM---------- 229
GD I++ +WIDH T + G V G++A ++++NNY+
Sbjct: 149 YVWGGDAITLDDCDLVWIDHVTTARI--GRQHYVLGTSADNRVSLTNNYIDGVSDYSATC 206
Query: 230 --FHHNEVMLMGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCR-HGFFHIVNNIYTGWE 286
+H+ + L G +D VT+ N+ R P+ + + H VNN +
Sbjct: 207 DGYHYWAIYLDGDAD--------LVTMKGNYIYH-TSGRSPKVQDNTLLHAVNNYWYDIS 257
Query: 287 MYAIGGSANPTINSQGNVF 305
+A + ++GNVF
Sbjct: 258 GHAFEIGEGGYVLAEGNVF 276
>pdb|1IDJ|A Chain A, Pectin Lyase A
pdb|1IDJ|B Chain B, Pectin Lyase A
Length = 359
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 45/199 (22%), Positives = 79/199 (39%), Gaps = 42/199 (21%)
Query: 123 LVMNSYKTIDGRGFNVQMSNGPCISIYNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPR 182
+ + S K++ G G + + + NIII NI + D P+
Sbjct: 104 ITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDI---------------NPK 148
Query: 183 GRSDGDGISIFGSRDIWIDHCTFSHCYDGLIDIVYGSTA---ITISNNYM---------- 229
GD I++ +WIDH T + G V G++A ++++NNY+
Sbjct: 149 YVWGGDAITLDDCDLVWIDHVTTARI--GRQHYVLGTSADNRVSLTNNYIDGVSDYSATC 206
Query: 230 --FHHNEVMLMGHSDDFSADKNMQVTIAFNFFGDGLVQRMPRCR-HGFFHIVNNIYTGWE 286
+H+ + L G +D VT+ N+ R P+ + + H VNN +
Sbjct: 207 DGYHYWGIYLDGDAD--------LVTMKGNYIYH-TSGRSPKVQDNTLLHCVNNYFYDIS 257
Query: 287 MYAIGGSANPTINSQGNVF 305
+A + ++GNVF
Sbjct: 258 GHAFEIGEGGYVLAEGNVF 276
>pdb|3TIH|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
pdb|3TIH|B Chain B, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
pdb|3TIH|C Chain C, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
pdb|3TIH|D Chain D, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
Length = 345
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 6/95 (6%)
Query: 89 PVDPIPGSLRYAVIQEEPLWIIFDHDMVINLKQELVMNSYKTIDGRGFNVQMSNGPCISI 148
P DP P L A + E + ++ +DMV + ++++ +++ V+++ G I+
Sbjct: 33 PTDPDPQELVMANVTEN--FNMWKNDMVDQMHEDIISLWDQSLKP---CVKLTGGSTIT- 86
Query: 149 YNVSNIIIHNIYIHDCVPAGSAVVRDSPKHYGPRG 183
+ I IH C PAG A+++ + K + +G
Sbjct: 87 QACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKG 121
>pdb|3VNG|A Chain A, Crystal Structure Of Keap1 In Complex With Synthetic
Small Molecular Based On A Co-crystallization
pdb|3VNH|A Chain A, Crystal Structure Of Keap1 Soaked With Synthetic Small
Molecular
Length = 309
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 19/36 (52%)
Query: 41 NPIDDCWRCDSEWESNRKALADCAVGFGRNAVGGRD 76
NP D W ++ + R LA C VG AVGGR+
Sbjct: 46 NPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGGRN 81
>pdb|3CR8|A Chain A, Hexameric Aps Kinase From Thiobacillus Denitrificans
pdb|3CR8|B Chain B, Hexameric Aps Kinase From Thiobacillus Denitrificans
pdb|3CR8|C Chain C, Hexameric Aps Kinase From Thiobacillus Denitrificans
Length = 552
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 28/68 (41%)
Query: 295 NPTINSQGNVFIASNDESTKEVTKHEIISEDDEWKKWNWRSEGDLMLNGAFFTPSGQETP 354
N I G + D +E KHE +S W + E ++++ GA+ +G T
Sbjct: 3 NQLIEPYGGTLVNLIDPEKREALKHEALSLPSLDLDWQQQCELEMLMTGAYSPLTGFMTR 62
Query: 355 ASYMKASS 362
A + S
Sbjct: 63 AQCARVES 70
>pdb|1U6D|X Chain X, Crystal Structure Of The Kelch Domain Of Human Keap1
pdb|2FLU|X Chain X, Crystal Structure Of The Kelch-Neh2 Complex
Length = 308
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 19/36 (52%)
Query: 41 NPIDDCWRCDSEWESNRKALADCAVGFGRNAVGGRD 76
NP D W ++ + R LA C VG AVGGR+
Sbjct: 45 NPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGGRN 80
>pdb|2V6O|A Chain A, Structure Of Schistosoma Mansoni Thioredoxin-Glutathione
Reductase (Smtgr)
Length = 596
Score = 28.5 bits (62), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 175 SPKHYGPRGRSDGDGISIFGSRDIWIDHCTF 205
+P YG G S+ D I +G +DI + H F
Sbjct: 475 TPLEYGACGLSEEDAIEKYGDKDIEVYHSNF 505
>pdb|2X8C|A Chain A, Thioredoxin Glutathione Reductase From Schistosoma Mansoni
With The Reduced C-Terminal End
pdb|2X8C|B Chain B, Thioredoxin Glutathione Reductase From Schistosoma Mansoni
With The Reduced C-Terminal End
pdb|2X8G|A Chain A, Oxidized Thioredoxin Glutathione Reductase From
Schistosoma Mansoni
pdb|2X8H|A Chain A, Thioredoxin Glutathione Reductase From Schistosoma Mansoni
In Complex With Gsh
pdb|2X99|A Chain A, Thioredoxin Glutathione Reductase From Schistosoma Mansoni
In Complex With Nadph
Length = 598
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 175 SPKHYGPRGRSDGDGISIFGSRDIWIDHCTF 205
+P YG G S+ D I +G +DI + H F
Sbjct: 475 TPLEYGACGLSEEDAIEKYGDKDIEVYHSNF 505
>pdb|3H4K|A Chain A, Crystal Structure Of The Wild Type Thioredoxin Glutatione
Reductase From Schistosoma Mansoni In Complex With
Auranofin
Length = 598
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 175 SPKHYGPRGRSDGDGISIFGSRDIWIDHCTF 205
+P YG G S+ D I +G +DI + H F
Sbjct: 475 TPLEYGACGLSEEDAIEKYGDKDIEVYHSNF 505
>pdb|1NLT|A Chain A, The Crystal Structure Of Hsp40 Ydj1
Length = 248
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 41 NPIDDCWRCDSEWESNRKALADCAVGFGRNAVGGRDGEIYIVKSKDDDPVDPIPGSLRYA 100
+P D C C+ + N + + + V G +DG+ + K + D D IPG + +
Sbjct: 94 DPKDRCKSCNGKKVENERKILEVHV-----EPGMKDGQRIVFKGEADQAPDVIPGDVVF- 147
Query: 101 VIQEEP 106
++ E P
Sbjct: 148 IVSERP 153
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
0.320 0.137 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,867,811
Number of Sequences: 62578
Number of extensions: 516960
Number of successful extensions: 1164
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1108
Number of HSP's gapped (non-prelim): 29
length of query: 390
length of database: 14,973,337
effective HSP length: 101
effective length of query: 289
effective length of database: 8,652,959
effective search space: 2500705151
effective search space used: 2500705151
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: 52 (24.6 bits)