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= 013757
(437 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 = 309 bits (791), Expect = 3e-84, Method: Compositional matrix adjust.
Identities = 162/346 (46%), Positives = 214/346 (61%), Gaps = 8/346 (2%)
Query: 90 NPIDQCWRCDRNWANNRKRLADCAQGFGRGTIGGKNGPFYVVTNPADDDLVNPKPGTLRH 149
NPID CWR D NW NR +LADCA GFG T+GGK G FY VT+ DD+ VNP PGTLR+
Sbjct: 2 NPIDSCWRGDSNWDQNRMKLADCAVGFGSSTMGGKGGDFYTVTS-TDDNPVNPTPGTLRY 60
Query: 150 AVIQERPLWITFAHDMVIRLSEELLITSDKTIDARGSNVQIYNGAQ-ITMQFVKNIIIHG 208
+E+ LWI F+ +M I+L L + KTID RG++V + NG + M+ V ++I+H
Sbjct: 61 GATREKALWIIFSQNMNIKLKMPLYVAGHKTIDGRGADVHLGNGGPCLFMRKVSHVILHS 120
Query: 209 LHIRKTKAGKGG--MIRDSVSHHGFRSSSDGDGISMFGASHIWIDHVSMSGCQDGLIDAV 266
LHI G ++ +S+ + DGD I+M ++ WIDH S+S C DGLID
Sbjct: 121 LHIHGCNTSVLGDVLVSESIGVEPVHAQ-DGDAITMRNVTNAWIDHNSLSDCSDGLIDVT 179
Query: 267 MGSTAITVSNSHFTHQDHVMLLGASDGHPQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAH 326
+GST IT+SN+HF + VMLLG D + D M+VTVAFN FG QRMPR R+G H
Sbjct: 180 LGSTGITISNNHFFNHHKVMLLGHDDTYDDDKSMKVTVAFNQFGPNAGQRMPRARYGLVH 239
Query: 327 VVNNDYTHWLMYAIGGSQHPTILSQGNRFLASNSHHSKEVTKR-DSSPQSVWKTWNWRSE 385
V NN+Y W +YAIGGS +PTILS+GN F A + + KEVTKR S W WRS
Sbjct: 240 VANNNYDPWNIYAIGGSSNPTILSEGNSFTAPSESYKKEVTKRIGCESPSACANWVWRST 299
Query: 386 MDLMMNGAFFVESG-SDVRNV-NRQDVIPAKPGKFASQMTRFSGAL 429
D +NGA+FV SG ++ N+ N + + G A Q+T+ +G +
Sbjct: 300 RDAFINGAYFVSSGKTEETNIYNSNEAFKVENGNAAPQLTKNAGVV 345
>pdb|3ZSC|A Chain A, Catalytic Function And Substrate Recognition Of The
Pectate Lyase From Thermotoga Maritima
Length = 340
Score = 92.4 bits (228), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 71/231 (30%), Positives = 104/231 (45%), Gaps = 24/231 (10%)
Query: 118 RGTIGGKNGPFYVVTNPADDDLVNPKPGTLRHAVIQERPLWITFAHDMVIRLSEELLITS 177
GT+GG G V + L E I +V E+ + S
Sbjct: 19 EGTVGGLGGEIVFVRTAEE----------LEKYTTAEGKYVIVVDGTIVFEPKREIKVLS 68
Query: 178 DKTIDARGSNVQIYNGAQITMQFVKNIIIHGLHIRKTKAGKGGMIRDSVSHHGFRSSSDG 237
DKTI G N G + ++ +N+II +H +G + D + D
Sbjct: 69 DKTI--VGINDAKIVGGGLVIKDAQNVIIRNIHF------EGFYMEDDPRGKKY----DF 116
Query: 238 DGISMFGASHIWIDHVSMSGCQDGLIDAVMGSTAITVSNSHFTHQDHVMLLGASDGH-PQ 296
D I++ + HIWIDH++ DG +D S ITVS + F D V L+G+SD P+
Sbjct: 117 DYINVENSHHIWIDHITFVNGNDGAVDIKKYSNYITVSWNKFVDHDKVSLVGSSDKEDPE 176
Query: 297 DSIMQVTVAFNH-FGKQLVQRMPRVRFGFAHVVNNDYTHWLMYAIGGSQHP 346
+ V ++H + K L+QRMPR+RFG AHV NN Y+ L + G+ P
Sbjct: 177 QAGQAYKVTYHHNYFKNLIQRMPRIRFGMAHVFNNFYSMGLRTGVSGNVFP 227
>pdb|1PCL|A Chain A, Unusual Structural Features In The Parallel Beta-Helix In
Pectate Lyases
Length = 355
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 63/218 (28%), Positives = 100/218 (45%), Gaps = 42/218 (19%)
Query: 172 ELLITSDKTIDARGSNVQIYNGAQITMQFVKNIIIHGLHIRKTKAGKGGMIRDSVSHHGF 231
++ I S+ TI GSN + NG+ + ++ VKN+I+ L+I D H+
Sbjct: 75 QISIPSNTTIIGVGSNGKFTNGS-LVIKGVKNVILRNLYIETP--------VDVAPHY-- 123
Query: 232 RSSSDG-----DGISMFGASHIWIDHVSMSGCQ-----------------DGLIDAVMGS 269
S DG D + ++++W+DHV++S DG +D GS
Sbjct: 124 -ESGDGWNAEWDAAVIDNSTNVWVDHVTISDGSFTDDKYTTKDGEKYVQHDGALDIKKGS 182
Query: 270 TAITVSNSHFTHQDHVMLLGASDGHPQDSIMQVTVAF-NHFGKQLVQRMPRVRFGFAHVV 328
+T+S S F D +L+G SD + ++ V F N+ ++ +R PRVRFG H
Sbjct: 183 DYVTISYSRFELHDKTILIGHSDSNGSQDSGKLRVTFHNNVFDRVTERAPRVRFGSIHAY 242
Query: 329 NNDY-------THWLMYAIGGSQHPTILSQGNRFLASN 359
NN Y + +Y+ G +ILS+ N F SN
Sbjct: 243 NNVYLGDVKHSVYPYLYSFGLGTSGSILSESNSFTLSN 280
>pdb|1VBL|A Chain A, Structure Of The Thermostable Pectate Lyase Pl 47
Length = 416
Score = 75.5 bits (184), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 53/146 (36%), Positives = 74/146 (50%), Gaps = 25/146 (17%)
Query: 234 SSDGDGISMFGASHIWIDHVSMSGCQ-----------------DGLIDAVMGSTAITVSN 276
+S+ D IS+ G+SHIWIDH + + DG +D S IT+S
Sbjct: 186 NSEYDSISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQHDGALDIKNSSDFITISY 245
Query: 277 SHFTHQDHVMLLGASDGHPQDS-IMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDYT-- 333
+ FT+ D V L+GASD DS ++VT+ N++ K + QR+PRVRFG H+ NN Y
Sbjct: 246 NVFTNHDKVTLIGASDSRMADSGHLRVTLHHNYY-KNVTQRLPRVRFGQVHIYNNYYEFS 304
Query: 334 ----HWLMYAIGGSQHPTILSQGNRF 355
+ YA G I +Q N F
Sbjct: 305 NLADYDFQYAWGVGVFSQIYAQNNYF 330
>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 = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 64/229 (27%), Positives = 102/229 (44%), Gaps = 42/229 (18%)
Query: 168 RLSEELLITSDKTIDARGSNVQIYNGAQIT--MQFVKNIIIHGLHIRKTKAGKGGMIRDS 225
+ ++ I ++ T+ G++ + NG+ I N+II ++I+ D
Sbjct: 78 KARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTP--------IDV 129
Query: 226 VSHH----GFRSSSDGDGISMFGASHIWIDHVSMSGCQ-----------------DGLID 264
H+ G+ + D I+ GA H+WIDHV++S DG +D
Sbjct: 130 EPHYEKGDGWNAEWDAMNITN-GAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALD 188
Query: 265 AVMGSTAITVSNSHFTHQDHVMLLGASD--GHPQDSIMQVTVAFNHFGKQLVQRMPRVRF 322
GS +T+SNS D ML+G SD G + VT+ FN+ ++ +R PRVR+
Sbjct: 189 IKRGSDYVTISNSLIDQHDKTMLIGHSDSNGSQDKGKLHVTL-FNNVFNRVTERAPRVRY 247
Query: 323 GFAHVVNN-------DYTHWLMYAIGGSQHPTILSQGNRFLASNSHHSK 364
G H NN D + Y+ G ++LS+GN F +N SK
Sbjct: 248 GSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASK 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 = 69.3 bits (168), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 62/228 (27%), Positives = 100/228 (43%), Gaps = 40/228 (17%)
Query: 168 RLSEELLITSDKTIDARGSNVQIYNGAQIT--MQFVKNIIIHGLHIRKTKAGKGGMIRDS 225
+ ++ I ++ T+ G++ + NG+ I N+II ++I+ D
Sbjct: 78 KARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTP--------IDV 129
Query: 226 VSHH----GFRSSSDGDGISMFGASHIWIDHVSMSGCQ-----------------DGLID 264
H+ G+ + D I+ GA H+WIDHV++S DG +D
Sbjct: 130 EPHYEKGDGWNAEWDAMNITN-GAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALD 188
Query: 265 AVMGSTAITVSNSHFTHQDHVMLLGASDGH-PQDSIMQVTVAFNHFGKQLVQRMPRVRFG 323
GS +T+SNS D ML+G +D + QD FN+ ++ +R PRVR+G
Sbjct: 189 IKRGSDYVTISNSLIDQHDKTMLIGHNDTNSAQDKGKLHVTLFNNVFNRVTERAPRVRYG 248
Query: 324 FAHVVNN-------DYTHWLMYAIGGSQHPTILSQGNRFLASNSHHSK 364
H NN D + Y+ G ++LS+GN F +N SK
Sbjct: 249 SIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASK 296
>pdb|1BN8|A Chain A, Bacillus Subtilis Pectate Lyase
Length = 420
Score = 65.5 bits (158), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 45/141 (31%), Positives = 67/141 (47%), Gaps = 26/141 (18%)
Query: 238 DGISMFGASHIWIDHVSMSGCQ-----------------DGLIDAVMGSTAITVSNSHFT 280
D I++ G +HIWIDH + + DG DA G+ IT+S +++
Sbjct: 205 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 264
Query: 281 HQDHVMLLGASDGH-PQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDY------- 332
D + G+SD D +++T+ N + K +VQR PRVRFG HV NN Y
Sbjct: 265 DHDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQRAPRVRFGQVHVYNNYYEGSTSSS 323
Query: 333 THWLMYAIGGSQHPTILSQGN 353
++ YA G + I +Q N
Sbjct: 324 SYPFSYAWGIGKSSKIYAQNN 344
>pdb|3KRG|A Chain A, Structural Insights Into Substrate Specificity And The
Anti Beta-Elimination Mechanism Of Pectate Lyase
Length = 399
Score = 65.1 bits (157), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 45/141 (31%), Positives = 67/141 (47%), Gaps = 26/141 (18%)
Query: 238 DGISMFGASHIWIDHVSMSGCQ-----------------DGLIDAVMGSTAITVSNSHFT 280
D I++ G +HIWIDH + + DG DA G+ IT+S +++
Sbjct: 184 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 243
Query: 281 HQDHVMLLGASDGH-PQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDY------- 332
D + G+SD D +++T+ N + K +VQR PRVRFG HV NN Y
Sbjct: 244 DHDASSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQRAPRVRFGQVHVYNNYYEGSTSSS 302
Query: 333 THWLMYAIGGSQHPTILSQGN 353
++ YA G + I +Q N
Sbjct: 303 SYPFSYAWGIGKSSKIYAQNN 323
>pdb|2BSP|A Chain A, Bacillus Subtilis Pectate Lyase R279k Mutant
Length = 420
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 44/141 (31%), Positives = 67/141 (47%), Gaps = 26/141 (18%)
Query: 238 DGISMFGASHIWIDHVSMSGCQ-----------------DGLIDAVMGSTAITVSNSHFT 280
D I++ G +HIWIDH + + DG DA G+ IT+S +++
Sbjct: 205 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 264
Query: 281 HQDHVMLLGASDGH-PQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDY------- 332
D + G+SD D +++T+ N + K +VQ+ PRVRFG HV NN Y
Sbjct: 265 DHDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQKAPRVRFGQVHVYNNYYEGSTSSS 323
Query: 333 THWLMYAIGGSQHPTILSQGN 353
++ YA G + I +Q N
Sbjct: 324 SYPFSYAWGIGKSSKIYAQNN 344
>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 = 62.8 bits (151), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 44/141 (31%), Positives = 66/141 (46%), Gaps = 26/141 (18%)
Query: 238 DGISMFGASHIWIDHVSMSGCQ-----------------DGLIDAVMGSTAITVSNSHFT 280
D I++ G +HIWIDH + + DG DA G+ IT+S +++
Sbjct: 184 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 243
Query: 281 HQDHVMLLGASDGH-PQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDY------- 332
D + G+SD D +++T+ N + K +VQ PRVRFG HV NN Y
Sbjct: 244 DHDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQAAPRVRFGQVHVYNNYYEGSTSSS 302
Query: 333 THWLMYAIGGSQHPTILSQGN 353
++ YA G + I +Q N
Sbjct: 303 SYPFSYAWGIGKSSKIYAQNN 323
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 48/167 (28%), Positives = 69/167 (41%), Gaps = 21/167 (12%)
Query: 231 FRSSSDGDGISMFG-----ASHIWIDH----VSMSGCQ-------DGLIDAVMGSTAITV 274
+ D D IS+ G S IW+DH S++ C DG ID G +TV
Sbjct: 107 LQGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTV 166
Query: 275 SNSHFTHQDHVMLLGASDGHPQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDYTH 334
S ++ + V L G SD ++S + T N F + + R+P RFG +H+ NN + +
Sbjct: 167 SYNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRFGLSHIYNNYFNN 225
Query: 335 WLMYAIGGSQHPTILSQGNRFLASNSHHSKEVTKRDSSPQSVWKTWN 381
I + N F + VT RDSS W N
Sbjct: 226 VTTSGINVRMGGIAKIESNYF----ENIKNPVTSRDSSEIGYWDLIN 268
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 48/167 (28%), Positives = 69/167 (41%), Gaps = 21/167 (12%)
Query: 231 FRSSSDGDGISMFG-----ASHIWIDH----VSMSGCQ-------DGLIDAVMGSTAITV 274
+ D D IS+ G S IW+DH S++ C DG ID G +TV
Sbjct: 107 LQGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTV 166
Query: 275 SNSHFTHQDHVMLLGASDGHPQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDYTH 334
S ++ + V L G SD ++S + T N F + + R+P RFG +H+ NN + +
Sbjct: 167 SYNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRFGLSHIYNNYFNN 225
Query: 335 WLMYAIGGSQHPTILSQGNRFLASNSHHSKEVTKRDSSPQSVWKTWN 381
I + N F + VT RDSS W N
Sbjct: 226 VTTSGINVRMGGIAKIESNYF----ENIKNPVTSRDSSEIGYWDLIN 268
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/167 (28%), Positives = 68/167 (40%), Gaps = 21/167 (12%)
Query: 231 FRSSSDGDGISMFG-----ASHIWIDH----VSMSGCQ-------DGLIDAVMGSTAITV 274
+ D D IS+ G S IW+DH S++ C DG ID G +TV
Sbjct: 107 LQGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTV 166
Query: 275 SNSHFTHQDHVMLLGASDGHPQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDYTH 334
S ++ + V L G SD ++S + T N F + + R+P R G +H+ NN + +
Sbjct: 167 SYNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRRGLSHIYNNYFNN 225
Query: 335 WLMYAIGGSQHPTILSQGNRFLASNSHHSKEVTKRDSSPQSVWKTWN 381
I + N F + VT RDSS W N
Sbjct: 226 VTTSGINVRMGGIAKIESNYF----ENIKNPVTSRDSSEIGYWDLIN 268
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 65/148 (43%), Gaps = 26/148 (17%)
Query: 191 YNGAQITMQFVKNIIIHGLHIRKTKAGKGGMIR---DS----VSHHGFRSSSDGDGISMF 243
++G I + NIII + I + G+G I DS + H+ F S G+G S +
Sbjct: 92 FDGIGIRLSNAHNIIIQNVSIHHVREGEGTAIEVTDDSKNVWIDHNEFYSEFPGNGDSDY 151
Query: 244 GASHIWIDHVSMSGCQDGLIDAVMGSTAITVSNSHFTHQDHVMLLGASDGHPQDSIMQVT 303
DGL+D + ITVS + F + ML+G +D S+
Sbjct: 152 ---------------YDGLVDMKRNAEYITVSWNKFENHWKTMLVGHTD---NASLAPDK 193
Query: 304 VAFNH-FGKQLVQRMPRVRFGFAHVVNN 330
+ ++H + L R+P +R+ H+ NN
Sbjct: 194 ITYHHNYFNNLNSRVPLIRYADVHMFNN 221
>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 = 35.0 bits (79), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 34/135 (25%), Positives = 56/135 (41%), Gaps = 17/135 (12%)
Query: 234 SSDGDGISMFGASHIWIDHVSMSGCQ---DGL----------IDAVMGSTAITVSNSHFT 280
+ DGD I + + ++W+DH + DG +D S +TVS ++
Sbjct: 127 AKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIH 186
Query: 281 HQDHVMLLGASDGHPQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDYTHWLMYAI 340
V L G+S D+ +T N++ + R+P R G H NN YT+ +
Sbjct: 187 GVKKVGLDGSSS---SDTGRNITYHHNYY-NDVNARLPLQRGGLVHAYNNLYTNITGSGL 242
Query: 341 GGSQHPTILSQGNRF 355
Q+ L + N F
Sbjct: 243 NVRQNGQALIENNWF 257
>pdb|2EWE|A Chain A, Crystal Structure Of Pectate Lyase C R218k Mutant In
Complex With Pentagalacturonic Acid
Length = 353
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 33/135 (24%), Positives = 56/135 (41%), Gaps = 17/135 (12%)
Query: 234 SSDGDGISMFGASHIWIDHVSMSGCQ---DGL----------IDAVMGSTAITVSNSHFT 280
+ DGD I + + ++W+DH + DG +D S +TVS ++
Sbjct: 127 AKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIH 186
Query: 281 HQDHVMLLGASDGHPQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNNDYTHWLMYAI 340
V L G+S D+ +T N++ + ++P R G H NN YT+ +
Sbjct: 187 GVKKVGLDGSSS---SDTGRNITYHHNYY-NDVNAKLPLQRGGLVHAYNNLYTNITGSGL 242
Query: 341 GGSQHPTILSQGNRF 355
Q+ L + N F
Sbjct: 243 NVRQNGQALIENNWF 257
>pdb|1QCX|A Chain A, Pectin Lyase B
Length = 359
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 44/168 (26%), Positives = 77/168 (45%), Gaps = 28/168 (16%)
Query: 205 IIHGLHIRKTKAGKGGMIRD-SVSHHGFRSSSDGDGISMFGASHIWIDHVSMSGCQDGLI 263
+I G +R K +I++ +V+ + GD I++ + +WIDHV+ + + G
Sbjct: 120 VIKGKGLRVVSGAKNVIIQNIAVTDINPKYVWGGDAITVDDSDLVWIDHVTTA--RIGRQ 177
Query: 264 DAVMGSTA---ITVSNSHFT------------HQDHVMLLGASDGHPQDSIMQVTVAFNH 308
V+G++A +T+S S H V L G++D VT+ N+
Sbjct: 178 HIVLGTSADNRVTISYSLIDGRSDYSATCNGHHYWGVYLDGSND--------MVTLKGNY 229
Query: 309 FGKQLVQRMPRVRFG-FAHVVNNDYTHWLMYAIGGSQHPTILSQGNRF 355
F L RMP+V+ H VNN + ++ +A +L++GN F
Sbjct: 230 F-YNLSGRMPKVQGNTLLHAVNNLFHNFDGHAFEIGTGGYVLAEGNVF 276
>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
Length = 428
Score = 31.6 bits (70), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 134 PADDDLVNPKPGTLRHAVIQERPLWITFAHDMVIRLSEELLITSDKTIDARGSNVQIYNG 193
PAD L P+P R I+E P + D ++ L+E+LL + +D + + + G
Sbjct: 89 PADAVLQKPQPQLYR--PIEETPCHFISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLG 146
Query: 194 AQITMQF---VKNIIIHGLHIR 212
MQ ++ II L +R
Sbjct: 147 LTCLMQISTRTEDFIIDTLELR 168
>pdb|1O89|A Chain A, Crystal Structure Of E. Coli K-12 Yhdh
pdb|1O8C|A Chain A, Crystal Structure Of E. Coli K-12 Yhdh With Bound Nadph
pdb|1O8C|B Chain B, Crystal Structure Of E. Coli K-12 Yhdh With Bound Nadph
pdb|1O8C|C Chain C, Crystal Structure Of E. Coli K-12 Yhdh With Bound Nadph
pdb|1O8C|D Chain D, Crystal Structure Of E. Coli K-12 Yhdh With Bound Nadph
Length = 345
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 33/74 (44%)
Query: 271 AITVSNSHFTHQDHVMLLGASDGHPQDSIMQVTVAFNHFGKQLVQRMPRVRFGFAHVVNN 330
A+ + + FT VM L + PQD + VT A G V + ++ + V
Sbjct: 142 AMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGR 201
Query: 331 DYTHWLMYAIGGSQ 344
+ TH + ++G S+
Sbjct: 202 ESTHEYLKSLGASR 215
>pdb|2HRU|A Chain A, T. Maritima Purl Complexed With Adp
pdb|2HRY|A Chain A, T. Maritima Purl Complexed With Amppcp
Length = 603
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 311 KQLVQRMPRVRF-GFAHVVNNDYTHWLMYAIGGSQHPTILSQGNRFLASNSHHSKEVTKR 369
K+ ++R+P+ F G A VVN D + + + I + HP+ + N ++V
Sbjct: 39 KKYIRRLPKTGFEGNAGVVNLDDYYSVAFKIESANHPSAIEPYNGAATGVGGIIRDVLAM 98
Query: 370 DSSPQSVWKTWNWRSEMDLMMNG 392
+ P +++ + + +D ++ G
Sbjct: 99 GARPTAIFDSLHMSRIIDGIIEG 121
>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
Length = 428
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 134 PADDDLVNPKPGTLRHAVIQERPLWITFAHDMVIRLSEELLITSDKTIDARGSNVQIYNG 193
PAD L P+P R I+E P + D ++ L+E+LL + ++ + + + G
Sbjct: 89 PADAVLQKPQPQLYR--PIEETPCHFISSLDELVELNEKLLNCQEFAVNLEHHSYRSFLG 146
Query: 194 AQITMQF---VKNIIIHGLHIR 212
MQ ++ II L +R
Sbjct: 147 LTCLMQISTRTEDFIIDTLELR 168
>pdb|2HPP|P Chain P, Structures Of The Noncovalent Complexes Of Human And
Bovine Prothrombin Fragment 2 With Human Ppack-Thrombin
Length = 79
Score = 28.5 bits (62), Expect = 8.0, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 78 RGRPYTGRCAATNPIDQC--WRCDRNWANNRKR----LADCAQGFGRGTIGGKNGPF-YV 130
RGR Y GR A T +C W ++ A ++ + A+ F R G + G + YV
Sbjct: 5 RGREYRGRLAVTTSGSRCLAWSSEQAKALSKDQDFNPAVPLAENFCRNPDGDEEGAWCYV 64
Query: 131 VTNPADDDLVN 141
P D + N
Sbjct: 65 ADQPGDFEYCN 75
>pdb|4EI7|A Chain A, Crystal Structure Of Bacillus Cereus Tubz, Gdp-Form
pdb|4EI7|B Chain B, Crystal Structure Of Bacillus Cereus Tubz, Gdp-Form
pdb|4EI9|A Chain A, Crystal Structure Of Bacillus Cereus Tubz, Gtp-Form
pdb|4EI9|B Chain B, Crystal Structure Of Bacillus Cereus Tubz, Gtp-Form
Length = 389
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 21 ILKANTHDFDEVWQKRAENARRHALEAYHP----NPEEVVSSFNKHVHMMFE 68
++ N+ DF+++ K N R+ LE Y NP+ +F KH +FE
Sbjct: 52 LVNTNSQDFNKIEIKNTGNVRKIQLEGYEQGAARNPQVGEEAFVKHETKIFE 103
>pdb|4EI8|A Chain A, Crystal Structure Of Bacillus Cereus Tubz, Apo-Form
Length = 389
Score = 28.5 bits (62), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 21 ILKANTHDFDEVWQKRAENARRHALEAYHP----NPEEVVSSFNKHVHMMFE 68
++ N+ DF+++ K N R+ LE Y NP+ +F KH +FE
Sbjct: 52 LVNTNSQDFNKIEIKNTGNVRKIQLEGYEQGAARNPQVGEEAFVKHETKIFE 103
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
0.321 0.134 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,077,770
Number of Sequences: 62578
Number of extensions: 596730
Number of successful extensions: 1426
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1377
Number of HSP's gapped (non-prelim): 28
length of query: 437
length of database: 14,973,337
effective HSP length: 102
effective length of query: 335
effective length of database: 8,590,381
effective search space: 2877777635
effective search space used: 2877777635
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: 53 (25.0 bits)