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= 013239
(447 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 = 319 bits (818), Expect = 2e-87, Method: Compositional matrix adjust.
Identities = 157/314 (50%), Positives = 214/314 (68%), Gaps = 14/314 (4%)
Query: 99 NPIDDCWRCDSRWYLRRKRLADCAIGFGRNAIGGRDGRYYVVSDPGDDDAVNPKPGTLRH 158
NPID CWR DS W R +LADCA+GFG + +GG+ G +Y V+ DD+ VNP PGTLR+
Sbjct: 2 NPIDSCWRGDSNWDQNRMKLADCAVGFGSSTMGGKGGDFYTVTST-DDNPVNPTPGTLRY 60
Query: 159 AVIQDRPLWIVFKRDMVITLKQELIMNSFKTIDGRGVNVHIANGA-CITIQFITNVIIHG 217
+++ LWI+F ++M I LK L + KTIDGRG +VH+ NG C+ ++ +++VI+H
Sbjct: 61 GATREKALWIIFSQNMNIKLKMPLYVAGHKTIDGRGADVHLGNGGPCLFMRKVSHVILHS 120
Query: 218 INIHDCKPT--GNAMVRSS----PSHYGWRTMADGDAISIFGSSHIWIDHNSLSNCADGL 271
++IH C + G+ +V S P H DGDAI++ ++ WIDHNSLS+C+DGL
Sbjct: 121 LHIHGCNTSVLGDVLVSESIGVEPVH-----AQDGDAITMRNVTNAWIDHNSLSDCSDGL 175
Query: 272 IDAIMGSTAITVSNNYFTHHNEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCRH 331
ID +GST IT+SNN+F +H++VMLLGH D+Y DK M+VT+A+N FG QRMPR R+
Sbjct: 176 IDVTLGSTGITISNNHFFNHHKVMLLGHDDTYDDDKSMKVTVAFNQFGPNAGQRMPRARY 235
Query: 332 GYFHVVNNDYTHWVMYAIGGSANPTINSQGNRYLAPENTFAKEVTKRVD-TSTAVWRGWN 390
G HV NN+Y W +YAIGGS+NPTI S+GN + AP ++ KEVTKR+ S + W
Sbjct: 236 GLVHVANNNYDPWNIYAIGGSSNPTILSEGNSFTAPSESYKKEVTKRIGCESPSACANWV 295
Query: 391 WRSEGDMLLNGAYF 404
WRS D +NGAYF
Sbjct: 296 WRSTRDAFINGAYF 309
>pdb|3ZSC|A Chain A, Catalytic Function And Substrate Recognition Of The
Pectate Lyase From Thermotoga Maritima
Length = 340
Score = 83.2 bits (204), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 67/191 (35%), Positives = 93/191 (48%), Gaps = 16/191 (8%)
Query: 168 IVFKRDMVITLKQELIMNSFKTIDGRGVNVHIANGACITIQFITNVIIHGINIHDCKPTG 227
IV +V K+E+ + S KTI G+N G + I+ NVII I+
Sbjct: 50 IVVDGTIVFEPKREIKVLSDKTI--VGINDAKIVGGGLVIKDAQNVIIRNIHFEGF---- 103
Query: 228 NAMVRSSPSHYGWRTMADGDAISIFGSSHIWIDHNSLSNCADGLIDAIMGSTAITVSNNY 287
+ P + D D I++ S HIWIDH + N DG +D S ITVS N
Sbjct: 104 --YMEDDPRGKKY----DFDYINVENSHHIWIDHITFVNGNDGAVDIKKYSNYITVSWNK 157
Query: 288 FTHHNEVMLLGHSDSYTRDKVMQ---VTIAYNHFGEGLIQRMPRCRHGYFHVVNNDYTHW 344
F H++V L+G SD ++ Q VT +N+F + LIQRMPR R G HV NN Y+
Sbjct: 158 FVDHDKVSLVGSSDKEDPEQAGQAYKVTYHHNYF-KNLIQRMPRIRFGMAHVFNNFYSMG 216
Query: 345 VMYAIGGSANP 355
+ + G+ P
Sbjct: 217 LRTGVSGNVFP 227
>pdb|1VBL|A Chain A, Structure Of The Thermostable Pectate Lyase Pl 47
Length = 416
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 60/185 (32%), Positives = 91/185 (49%), Gaps = 36/185 (19%)
Query: 182 LIMNSFKTIDGRGVNVHIANGACITIQFITNVIIHGINIH-------DCKPTGNAMVRSS 234
+ + S +I G G + I G + I+ + NVII I + PT +
Sbjct: 128 VYVGSNTSIIGVGKDAKIKGGGFL-IKNVDNVIIRNIEFEAPLDYFPEWDPTDGTLGE-- 184
Query: 235 PSHYGWRTMADGDAISIFGSSHIWIDHNSLSNCA-----------------DGLIDAIMG 277
W + + D+ISI GSSHIWIDHN+ ++ DG +D
Sbjct: 185 -----WNS--EYDSISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQHDGALDIKNS 237
Query: 278 STAITVSNNYFTHHNEVMLLGHSDSYTRDKV-MQVTIAYNHFGEGLIQRMPRCRHGYFHV 336
S IT+S N FT+H++V L+G SDS D ++VT+ +N++ + + QR+PR R G H+
Sbjct: 238 SDFITISYNVFTNHDKVTLIGASDSRMADSGHLRVTLHHNYY-KNVTQRLPRVRFGQVHI 296
Query: 337 VNNDY 341
NN Y
Sbjct: 297 YNNYY 301
>pdb|1BN8|A Chain A, Bacillus Subtilis Pectate Lyase
Length = 420
Score = 72.0 bits (175), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 70/239 (29%), Positives = 104/239 (43%), Gaps = 40/239 (16%)
Query: 189 TIDGRGVNVHIANGACITIQFIT-NVIIHGINIHDCKPTGNAMVRSSPSHYGWRTMADGD 247
TI G G N + G Q + NVII I D + S W + D
Sbjct: 151 TIVGSGTNAKVVGG---NFQIKSDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDN- 206
Query: 248 AISIFGSSHIWIDHNSLSNCA-----------------DGLIDAIMGSTAITVSNNYFTH 290
I+I G +HIWIDH + ++ + DG DA G+ IT+S NY+
Sbjct: 207 -ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHD 265
Query: 291 HNEVMLLGHSDSYTRDK-VMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNNDY-------T 342
H++ + G SDS T D +++T+ +N + + ++QR PR R G HV NN Y +
Sbjct: 266 HDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQRAPRVRFGQVHVYNNYYEGSTSSSS 324
Query: 343 HWVMYAIGGSANPTINSQGNRYLAPENTFAKEVTKRVDTSTAVWRGWNWRSEGDMLLNG 401
+ YA G + I +Q N P + AK ++ V+ G + LLNG
Sbjct: 325 YPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTIS--------VFSGGTALYDSGTLLNG 375
>pdb|3KRG|A Chain A, Structural Insights Into Substrate Specificity And The
Anti Beta-Elimination Mechanism Of Pectate Lyase
Length = 399
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 70/239 (29%), Positives = 104/239 (43%), Gaps = 40/239 (16%)
Query: 189 TIDGRGVNVHIANGACITIQFIT-NVIIHGINIHDCKPTGNAMVRSSPSHYGWRTMADGD 247
TI G G N + G Q + NVII I D ++ S W + D
Sbjct: 130 TIVGSGTNAKVVGG---NFQIKSDNVIIRNIEFQDAYDYFPQWDPTAGSSGNWASQYDN- 185
Query: 248 AISIFGSSHIWIDHNSLSNCA-----------------DGLIDAIMGSTAITVSNNYFTH 290
I+I G +HIWIDH + ++ + DG DA G+ IT+S NY+
Sbjct: 186 -ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHD 244
Query: 291 HNEVMLLGHSDSYTRDK-VMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNNDY-------T 342
H+ + G SDS T D +++T+ +N + + ++QR PR R G HV NN Y +
Sbjct: 245 HDASSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQRAPRVRFGQVHVYNNYYEGSTSSSS 303
Query: 343 HWVMYAIGGSANPTINSQGNRYLAPENTFAKEVTKRVDTSTAVWRGWNWRSEGDMLLNG 401
+ YA G + I +Q N P + AK ++ V+ G + LLNG
Sbjct: 304 YPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTIS--------VFSGGTALYDSGTLLNG 354
>pdb|2BSP|A Chain A, Bacillus Subtilis Pectate Lyase R279k Mutant
Length = 420
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 69/239 (28%), Positives = 104/239 (43%), Gaps = 40/239 (16%)
Query: 189 TIDGRGVNVHIANGACITIQFIT-NVIIHGINIHDCKPTGNAMVRSSPSHYGWRTMADGD 247
TI G G N + G Q + NVII I D + S W + D
Sbjct: 151 TIVGSGTNAKVVGG---NFQIKSDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDN- 206
Query: 248 AISIFGSSHIWIDHNSLSNCA-----------------DGLIDAIMGSTAITVSNNYFTH 290
I+I G +HIWIDH + ++ + DG DA G+ IT+S NY+
Sbjct: 207 -ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHD 265
Query: 291 HNEVMLLGHSDSYTRDK-VMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNNDY-------T 342
H++ + G SDS T D +++T+ +N + + ++Q+ PR R G HV NN Y +
Sbjct: 266 HDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQKAPRVRFGQVHVYNNYYEGSTSSSS 324
Query: 343 HWVMYAIGGSANPTINSQGNRYLAPENTFAKEVTKRVDTSTAVWRGWNWRSEGDMLLNG 401
+ YA G + I +Q N P + AK ++ V+ G + LLNG
Sbjct: 325 YPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTIS--------VFSGGTALYDSGTLLNG 375
>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 = 69.3 bits (168), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 69/239 (28%), Positives = 103/239 (43%), Gaps = 40/239 (16%)
Query: 189 TIDGRGVNVHIANGACITIQFIT-NVIIHGINIHDCKPTGNAMVRSSPSHYGWRTMADGD 247
TI G G N + G Q + NVII I D + S W + D
Sbjct: 130 TIVGSGTNAKVVGG---NFQIKSDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDN- 185
Query: 248 AISIFGSSHIWIDHNSLSNCA-----------------DGLIDAIMGSTAITVSNNYFTH 290
I+I G +HIWIDH + ++ + DG DA G+ IT+S NY+
Sbjct: 186 -ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHD 244
Query: 291 HNEVMLLGHSDSYTRDK-VMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNNDY-------T 342
H++ + G SDS T D +++T+ +N + + ++Q PR R G HV NN Y +
Sbjct: 245 HDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQAAPRVRFGQVHVYNNYYEGSTSSSS 303
Query: 343 HWVMYAIGGSANPTINSQGNRYLAPENTFAKEVTKRVDTSTAVWRGWNWRSEGDMLLNG 401
+ YA G + I +Q N P + AK ++ V+ G + LLNG
Sbjct: 304 YPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTIS--------VFSGGTALYDSGTLLNG 354
>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 = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 64/212 (30%), Positives = 98/212 (46%), Gaps = 50/212 (23%)
Query: 189 TIDGRGVNVHIANGACIT--IQFITNVIIHGINIH---DCKPTGNAMVRSSPSHY----G 239
T+ G G + NG+ I NVII + I D +P HY G
Sbjct: 90 TVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEP-----------HYEKGDG 138
Query: 240 WRTMADGDAISIF-GSSHIWIDHNSLSNCA-----------------DGLIDAIMGSTAI 281
W A+ DA++I G+ H+WIDH ++S+ DG +D GS +
Sbjct: 139 WN--AEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYV 196
Query: 282 TVSNNYFTHHNEVMLLGHSDSY-TRDK-VMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNN 339
T+SN+ H++ ML+GHSDS ++DK + VT+ N F + +R PR R+G H NN
Sbjct: 197 TISNSLIDQHDKTMLIGHSDSNGSQDKGKLHVTLFNNVFNR-VTERAPRVRYGSIHSFNN 255
Query: 340 -------DYTHWVMYAIGGSANPTINSQGNRY 364
D + Y+ G + ++ S+GN +
Sbjct: 256 VFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSF 287
>pdb|1PCL|A Chain A, Unusual Structural Features In The Parallel Beta-Helix In
Pectate Lyases
Length = 355
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 60/218 (27%), Positives = 101/218 (46%), Gaps = 46/218 (21%)
Query: 179 KQELIMNSFKTIDGRGVNVHIANGACITIQFITNVIIHGINIH---DCKPTGNAMVRSSP 235
+ ++ + S TI G G N NG+ + I+ + NVI+ + I D P
Sbjct: 73 RSQISIPSNTTIIGVGSNGKFTNGSLV-IKGVKNVILRNLYIETPVDVAP---------- 121
Query: 236 SHY----GWRTMADGDAISIFGSSHIWIDHNSLSNCA-----------------DGLIDA 274
HY GW A+ DA I S+++W+DH ++S+ + DG +D
Sbjct: 122 -HYESGDGWN--AEWDAAVIDNSTNVWVDHVTISDGSFTDDKYTTKDGEKYVQHDGALDI 178
Query: 275 IMGSTAITVSNNYFTHHNEVMLLGHSDSYTRDKVMQVTIAY-NHFGEGLIQRMPRCRHGY 333
GS +T+S + F H++ +L+GHSDS ++ + + N+ + + +R PR R G
Sbjct: 179 KKGSDYVTISYSRFELHDKTILIGHSDSNGSQDSGKLRVTFHNNVFDRVTERAPRVRFGS 238
Query: 334 FHVVNN----DYTHWV---MYAIGGSANPTINSQGNRY 364
H NN D H V +Y+ G + +I S+ N +
Sbjct: 239 IHAYNNVYLGDVKHSVYPYLYSFGLGTSGSILSESNSF 276
>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 = 65.1 bits (157), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 62/212 (29%), Positives = 98/212 (46%), Gaps = 50/212 (23%)
Query: 189 TIDGRGVNVHIANGACIT--IQFITNVIIHGINIH---DCKPTGNAMVRSSPSHY----G 239
T+ G G + NG+ I NVII + I D +P HY G
Sbjct: 90 TVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEP-----------HYEKGDG 138
Query: 240 WRTMADGDAISIF-GSSHIWIDHNSLSNCA-----------------DGLIDAIMGSTAI 281
W A+ DA++I G+ H+WIDH ++S+ DG +D GS +
Sbjct: 139 WN--AEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYV 196
Query: 282 TVSNNYFTHHNEVMLLGHSDSYT-RDK-VMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNN 339
T+SN+ H++ ML+GH+D+ + +DK + VT+ N F + +R PR R+G H NN
Sbjct: 197 TISNSLIDQHDKTMLIGHNDTNSAQDKGKLHVTLFNNVFNR-VTERAPRVRYGSIHSFNN 255
Query: 340 -------DYTHWVMYAIGGSANPTINSQGNRY 364
D + Y+ G + ++ S+GN +
Sbjct: 256 VFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSF 287
>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 = 61.6 bits (148), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 60/111 (54%), Gaps = 17/111 (15%)
Query: 245 DGDAISIFGSS-----HIWIDHN----SLSNCA-------DGLIDAIMGSTAITVSNNYF 288
D D+IS+ G+S IW+DHN SL+ C+ DG ID G +TVS NY
Sbjct: 112 DADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYV 171
Query: 289 THHNEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNN 339
++ +V L G+SDS T++ + T +N F E + R+P R G H+ NN
Sbjct: 172 YNYQKVALNGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRRGLSHIYNN 221
>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 = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 60/111 (54%), Gaps = 17/111 (15%)
Query: 245 DGDAISIFGSS-----HIWIDHN----SLSNCA-------DGLIDAIMGSTAITVSNNYF 288
D D+IS+ G+S IW+DHN SL+ C+ DG ID G +TVS NY
Sbjct: 112 DADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYV 171
Query: 289 THHNEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNN 339
++ +V L G+SDS T++ + T +N F E + R+P R G H+ NN
Sbjct: 172 YNYQKVALNGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRFGLSHIYNN 221
>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 = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 60/111 (54%), Gaps = 17/111 (15%)
Query: 245 DGDAISIFGSS-----HIWIDHN----SLSNCA-------DGLIDAIMGSTAITVSNNYF 288
D D+IS+ G+S IW+DHN SL+ C+ DG ID G +TVS NY
Sbjct: 112 DADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYV 171
Query: 289 THHNEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNN 339
++ +V L G+SDS T++ + T +N F E + R+P R G H+ NN
Sbjct: 172 YNYQKVALNGYSDSDTKNSAARTTYHHNRF-ENVESRVPLQRFGLSHIYNN 221
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 62/213 (29%), Positives = 93/213 (43%), Gaps = 44/213 (20%)
Query: 189 TIDGRGVNVHIANGACITIQFITNVIIHGINIHDCKPTGNAMVRSSPSHYGWRTMADGDA 248
+I G G N +G I + N+II ++IH + +G A
Sbjct: 82 SIIGVGTNGEF-DGIGIRLSNAHNIIIQNVSIHHVRE------------------GEGTA 122
Query: 249 ISIFG-SSHIWIDHNSL---------SNCADGLIDAIMGSTAITVSNNYFTHHNEVMLLG 298
I + S ++WIDHN S+ DGL+D + ITVS N F +H + ML+G
Sbjct: 123 IEVTDDSKNVWIDHNEFYSEFPGNGDSDYYDGLVDMKRNAEYITVSWNKFENHWKTMLVG 182
Query: 299 HSD--SYTRDKVMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNNDYTHWVMYAIGGSANPT 356
H+D S DK +T +N+F L R+P R+ H+ NN + I +A
Sbjct: 183 HTDNASLAPDK---ITYHHNYF-NNLNSRVPLIRYADVHMFNNYFK-----DINDTA--- 230
Query: 357 INSQ-GNRYLAPENTFAKEVTKRVDTSTAVWRG 388
INS+ G R N F + + D +T +G
Sbjct: 231 INSRVGARVFVENNYFDNVGSGQADPTTGFIKG 263
>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 = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 34/112 (30%), Positives = 50/112 (44%), Gaps = 17/112 (15%)
Query: 245 DGDAISIFGSSHIWIDHNSL-------------SNCADGLIDAIMGSTAITVSNNYFTHH 291
DGD I + S ++W+DHN L + +D S +TVS NY
Sbjct: 129 DGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGV 188
Query: 292 NEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNNDYTH 343
+V L G S S D +T +N++ + + R+P R G H NN YT+
Sbjct: 189 KKVGLDGSSSS---DTGRNITYHHNYYND-VNARLPLQRGGLVHAYNNLYTN 236
>pdb|2EWE|A Chain A, Crystal Structure Of Pectate Lyase C R218k Mutant In
Complex With Pentagalacturonic Acid
Length = 353
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 50/112 (44%), Gaps = 17/112 (15%)
Query: 245 DGDAISIFGSSHIWIDHNSL-------------SNCADGLIDAIMGSTAITVSNNYFTHH 291
DGD I + S ++W+DHN L + +D S +TVS NY
Sbjct: 129 DGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGV 188
Query: 292 NEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCRHGYFHVVNNDYTH 343
+V L G S S D +T +N++ + + ++P R G H NN YT+
Sbjct: 189 KKVGLDGSSSS---DTGRNITYHHNYYND-VNAKLPLQRGGLVHAYNNLYTN 236
>pdb|1QCX|A Chain A, Pectin Lyase B
Length = 359
Score = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 50/199 (25%), Positives = 83/199 (41%), Gaps = 42/199 (21%)
Query: 182 LIMNSFKTIDGRGVNVHIANGACITIQFITNVIIHGINIHDCKPTGNAMVRSSPSHYGWR 241
+ +NS K+I G+G I + NVII I + D P Y W
Sbjct: 104 ITVNSNKSIVGQGTKGVIKGKGLRVVSGAKNVIIQNIAVTDINP-----------KYVW- 151
Query: 242 TMADGDAISIFGSSHIWIDHNSLSNCADGLIDAIMGSTA---ITVSNNYFT--------- 289
GDAI++ S +WIDH ++ G ++G++A +T+S +
Sbjct: 152 ---GGDAITVDDSDLVWIDH--VTTARIGRQHIVLGTSADNRVTISYSLIDGRSDYSATC 206
Query: 290 ---HHNEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCR-HGYFHVVNNDYTHWV 345
H+ V L G +D VT+ N+F L RMP+ + + H VNN + ++
Sbjct: 207 NGHHYWGVYLDGSND--------MVTLKGNYF-YNLSGRMPKVQGNTLLHAVNNLFHNFD 257
Query: 346 MYAIGGSANPTINSQGNRY 364
+A + ++GN +
Sbjct: 258 GHAFEIGTGGYVLAEGNVF 276
>pdb|1IDK|A Chain A, Pectin Lyase A
Length = 359
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 55/223 (24%), Positives = 88/223 (39%), Gaps = 54/223 (24%)
Query: 182 LIMNSFKTIDGRGVNVHIANGACITIQFITNVIIHGINIHDCKPTGNAMVRSSPSHYGWR 241
+ + S K++ G G + I + N+II I + D P Y W
Sbjct: 104 ITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDINP-----------KYVWG 152
Query: 242 TMADGDAISIFGSSHIWIDHNSLSNCADGLIDAIMGSTA---ITVSNNYFT--------- 289
GDAI++ +WIDH ++ G ++G++A ++++NNY
Sbjct: 153 ----GDAITLDDCDLVWIDH--VTTARIGRQHYVLGTSADNRVSLTNNYIDGVSDYSATC 206
Query: 290 ---HHNEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCR-HGYFHVVNNDYTHWV 345
H+ + L G +D T M+ Y+ G R P+ + + H VNN +W
Sbjct: 207 DGYHYWAIYLDGDADLVT----MKGNYIYHTSG-----RSPKVQDNTLLHAVNN---YW- 253
Query: 346 MYAIGGSANPTINSQGNRYLAPENTFAKEVTKRVDTSTAVWRG 388
Y I G A +G LA N F + VDT + G
Sbjct: 254 -YDISGHAFEI--GEGGYVLAEGNVF-----QNVDTVLETYEG 288
>pdb|1IDJ|A Chain A, Pectin Lyase A
pdb|1IDJ|B Chain B, Pectin Lyase A
Length = 359
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 54/223 (24%), Positives = 86/223 (38%), Gaps = 54/223 (24%)
Query: 182 LIMNSFKTIDGRGVNVHIANGACITIQFITNVIIHGINIHDCKPTGNAMVRSSPSHYGWR 241
+ + S K++ G G + I + N+II I + D P Y W
Sbjct: 104 ITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDINP-----------KYVWG 152
Query: 242 TMADGDAISIFGSSHIWIDHNSLSNCADGLIDAIMGSTA---ITVSNNYFT--------- 289
GDAI++ +WIDH ++ G ++G++A ++++NNY
Sbjct: 153 ----GDAITLDDCDLVWIDH--VTTARIGRQHYVLGTSADNRVSLTNNYIDGVSDYSATC 206
Query: 290 ---HHNEVMLLGHSDSYTRDKVMQVTIAYNHFGEGLIQRMPRCR-HGYFHVVNNDYTHWV 345
H+ + L G +D T M+ Y+ G R P+ + + H VNN
Sbjct: 207 DGYHYWGIYLDGDADLVT----MKGNYIYHTSG-----RSPKVQDNTLLHCVNN-----Y 252
Query: 346 MYAIGGSANPTINSQGNRYLAPENTFAKEVTKRVDTSTAVWRG 388
Y I G A +G LA N F + VDT + G
Sbjct: 253 FYDISGHAFEI--GEGGYVLAEGNVF-----QNVDTVLETYEG 288
>pdb|3S5E|A Chain A, Crystal Structure Of Human Frataxin Variant W155r, One Of
The Friedreich's Ataxia Point Mutations
Length = 129
Score = 29.3 bits (64), Expect = 4.1, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 39 NEQLQSSNNSSMPERIEFDDEEWTHEH-AVDNPDEIAATVDMAIRNSTERRKLGY 92
N+Q++ S+ SS P+R ++ + W + H V + +AA + A++ + L Y
Sbjct: 70 NKQIRLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAY 124
>pdb|3S5D|A Chain A, Crystal Structure Of Human Frataxin Variant W155a
Length = 129
Score = 28.9 bits (63), Expect = 6.5, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 39 NEQLQSSNNSSMPERIEFDDEEWTHEH-AVDNPDEIAATVDMAIRNSTERRKLGY 92
N+Q+ S+ SS P+R ++ + W + H V + +AA + A++ + L Y
Sbjct: 70 NKQIALSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAY 124
>pdb|3T3J|A Chain A, 1.70 A Structure Of Friedreich's Ataxia Frataxin Variant
N146k
Length = 129
Score = 28.1 bits (61), Expect = 9.7, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 39 NEQLQSSNNSSMPERIEFDDEEWTHEH-AVDNPDEIAATVDMAIRNSTERRKLGY 92
N+Q+ S+ SS P+R ++ + W + H V + +AA + A++ + L Y
Sbjct: 70 NKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAY 124
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 0.136 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,845,411
Number of Sequences: 62578
Number of extensions: 581855
Number of successful extensions: 1302
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1255
Number of HSP's gapped (non-prelim): 30
length of query: 447
length of database: 14,973,337
effective HSP length: 102
effective length of query: 345
effective length of database: 8,590,381
effective search space: 2963681445
effective search space used: 2963681445
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)