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= 036607
(436 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 = 289 bits (740), Expect = 2e-78, Method: Compositional matrix adjust.
Identities = 152/348 (43%), Positives = 203/348 (58%), Gaps = 8/348 (2%)
Query: 87 NPIDKCWRCKENWAEDRQALAGCALXXXXXXXXXXXXXIYEVTDPSDNDMENPKVGTLRH 146
NPID CWR NW ++R LA CA+ Y VT DN + NP GTLR+
Sbjct: 2 NPIDSCWRGDSNWDQNRMKLADCAVGFGSSTMGGKGGDFYTVTSTDDNPV-NPTPGTLRY 60
Query: 147 AVIQKEPLWIIFAKDMNIKLQQELIVQGSKTIDGRGAKVHIANGAGIMLQFVKNVXXXXX 206
+++ LWIIF+++MNIKL+ L V G KTIDGRGA VH+ NG + F++ V
Sbjct: 61 GATREKALWIIFSQNMNIKLKMPLYVAGHKTIDGRGADVHLGNGGPCL--FMRKVSHVIL 118
Query: 207 XXXXXSPCSGGMIRDSV--DHVGKR--GQSDGDAVSIFGSSNIWLDHLTLSQAHDGLIDA 262
C+ ++ D + + +G DGDA+++ +N W+DH +LS DGLID
Sbjct: 119 HSLHIHGCNTSVLGDVLVSESIGVEPVHAQDGDAITMRNVTNAWIDHNSLSDCSDGLIDV 178
Query: 263 IQASTAITISNCHLSNHDKAILLGASDTFTEDKKMQVTVAFNRFDKGLVQRMPCVRFGFA 322
ST ITISN H NH K +LLG DT+ +DK M+VTVAFN+F QRMP R+G
Sbjct: 179 TLGSTGITISNNHFFNHHKVMLLGHDDTYDDDKSMKVTVAFNQFGPNAGQRMPRARYGLV 238
Query: 323 HVVNNDYNQWEMYAIGGLQGPTILSQGNRFFASNNQNAKEVTKRMNC-SPEEGKSWIWRS 381
HV NN+Y+ W +YAIGG PTILS+GN F A + KEVTKR+ C SP +W+WRS
Sbjct: 239 HVANNNYDPWNIYAIGGSSNPTILSEGNSFTAPSESYKKEVTKRIGCESPSACANWVWRS 298
Query: 382 EGDVLLNGAYFNSSGDPKKQIQYQMDDVIKPESGTEVERITKFAGALV 429
D +NGAYF SSG ++ Y ++ K E+G ++TK AG +
Sbjct: 299 TRDAFINGAYFVSSGKTEETNIYNSNEAFKVENGNAAPQLTKNAGVVT 346
>pdb|3ZSC|A Chain A, Catalytic Function And Substrate Recognition Of The
Pectate Lyase From Thermotoga Maritima
Length = 340
Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 50/138 (36%), Positives = 73/138 (52%), Gaps = 15/138 (10%)
Query: 229 RGQS-DGDAVSIFGSSNIWLDHLTLSQAHDGLIDAIQASTAITISNCHLSNHDKAILLGA 287
RG+ D D +++ S +IW+DH+T +DG +D + S IT+S +HDK L+G+
Sbjct: 110 RGKKYDFDYINVENSHHIWIDHITFVNGNDGAVDIKKYSNYITVSWNKFVDHDKVSLVGS 169
Query: 288 SDTFTEDKKMQ---VTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY----------NQWEM 334
SD ++ Q VT N F K L+QRMP +RFG AHV NN Y N + +
Sbjct: 170 SDKEDPEQAGQAYKVTYHHNYF-KNLIQRMPRIRFGMAHVFNNFYSMGLRTGVSGNVFPI 228
Query: 335 YAIGGLQGPTILSQGNRF 352
Y + G + +GN F
Sbjct: 229 YGVASAMGAKVHVEGNYF 246
>pdb|1VBL|A Chain A, Structure Of The Thermostable Pectate Lyase Pl 47
Length = 416
Score = 82.0 bits (201), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 62/179 (34%), Positives = 86/179 (48%), Gaps = 23/179 (12%)
Query: 170 LIVQGSKT-IDGRGAKVHIANGAGIMLQFVKNVXXXXXXXXXXSPCSGGMIRDSVDHVGK 228
++ GS T I G G I G G +++ V NV +P D D
Sbjct: 127 MVYVGSNTSIIGVGKDAKIK-GGGFLIKNVDNVIIRNIEFE--APLDYFPEWDPTDGTLG 183
Query: 229 RGQSDGDAVSIFGSSNIWLDHLTLS-----------------QAHDGLIDAIQASTAITI 271
S+ D++SI GSS+IW+DH T + Q HDG +D +S ITI
Sbjct: 184 EWNSEYDSISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQHDGALDIKNSSDFITI 243
Query: 272 SNCHLSNHDKAILLGASDTFTEDK-KMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
S +NHDK L+GASD+ D ++VT+ N + K + QR+P VRFG H+ NN Y
Sbjct: 244 SYNVFTNHDKVTLIGASDSRMADSGHLRVTLHHNYY-KNVTQRLPRVRFGQVHIYNNYY 301
>pdb|1BN8|A Chain A, Bacillus Subtilis Pectate Lyase
Length = 420
Score = 78.6 bits (192), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 43/113 (38%), Positives = 64/113 (56%), Gaps = 19/113 (16%)
Query: 235 DAVSIFGSSNIWLDHLTLS-----------------QAHDGLIDAIQASTAITISNCHLS 277
D ++I G ++IW+DH T + Q HDG DA + IT+S +
Sbjct: 205 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 264
Query: 278 NHDKAILLGASDTFT-EDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
+HDK+ + G+SD+ T +D K+++T+ NR+ K +VQR P VRFG HV NN Y
Sbjct: 265 DHDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQRAPRVRFGQVHVYNNYY 316
>pdb|2BSP|A Chain A, Bacillus Subtilis Pectate Lyase R279k Mutant
Length = 420
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 42/113 (37%), Positives = 64/113 (56%), Gaps = 19/113 (16%)
Query: 235 DAVSIFGSSNIWLDHLTLS-----------------QAHDGLIDAIQASTAITISNCHLS 277
D ++I G ++IW+DH T + Q HDG DA + IT+S +
Sbjct: 205 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 264
Query: 278 NHDKAILLGASDTFT-EDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
+HDK+ + G+SD+ T +D K+++T+ NR+ K +VQ+ P VRFG HV NN Y
Sbjct: 265 DHDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQKAPRVRFGQVHVYNNYY 316
>pdb|1PCL|A Chain A, Unusual Structural Features In The Parallel Beta-Helix In
Pectate Lyases
Length = 355
Score = 76.6 bits (187), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 67/223 (30%), Positives = 98/223 (43%), Gaps = 44/223 (19%)
Query: 165 KLQQELIVQGSKTIDGRGAKVHIANGAGIMLQFVKNVXXXXXXXXXXSPCSGGMIRDSVD 224
K + ++ + + TI G G+ NG+ ++++ VKNV I VD
Sbjct: 71 KARSQISIPSNTTIIGVGSNGKFTNGS-LVIKGVKNVILRNL-----------YIETPVD 118
Query: 225 HVGKRGQSDG-----DAVSIFGSSNIWLDHLTLSQA-----------------HDGLIDA 262
DG DA I S+N+W+DH+T+S HDG +D
Sbjct: 119 VAPHYESGDGWNAEWDAAVIDNSTNVWVDHVTISDGSFTDDKYTTKDGEKYVQHDGALDI 178
Query: 263 IQASTAITISNCHLSNHDKAILLGASDT--FTEDKKMQVTVAFNRFDKGLVQRMPCVRFG 320
+ S +TIS HDK IL+G SD+ + K++VT N FD+ + +R P VRFG
Sbjct: 179 KKGSDYVTISYSRFELHDKTILIGHSDSNGSQDSGKLRVTFHNNVFDR-VTERAPRVRFG 237
Query: 321 FAHVVNNDY-------NQWEMYAIGGLQGPTILSQGNRFFASN 356
H NN Y +Y+ G +ILS+ N F SN
Sbjct: 238 SIHAYNNVYLGDVKHSVYPYLYSFGLGTSGSILSESNSFTLSN 280
>pdb|3KRG|A Chain A, Structural Insights Into Substrate Specificity And The
Anti Beta-Elimination Mechanism Of Pectate Lyase
Length = 399
Score = 76.3 bits (186), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 42/113 (37%), Positives = 63/113 (55%), Gaps = 19/113 (16%)
Query: 235 DAVSIFGSSNIWLDHLTLS-----------------QAHDGLIDAIQASTAITISNCHLS 277
D ++I G ++IW+DH T + Q HDG DA + IT+S +
Sbjct: 184 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 243
Query: 278 NHDKAILLGASDTFT-EDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
+HD + + G+SD+ T +D K+++T+ NR+ K +VQR P VRFG HV NN Y
Sbjct: 244 DHDASSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQRAPRVRFGQVHVYNNYY 295
>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 = 75.9 bits (185), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 42/113 (37%), Positives = 63/113 (55%), Gaps = 19/113 (16%)
Query: 235 DAVSIFGSSNIWLDHLTLS-----------------QAHDGLIDAIQASTAITISNCHLS 277
D ++I G ++IW+DH T + Q HDG DA + IT+S +
Sbjct: 184 DNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYH 243
Query: 278 NHDKAILLGASDTFT-EDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
+HDK+ + G+SD+ T +D K+++T+ NR+ K +VQ P VRFG HV NN Y
Sbjct: 244 DHDKSSIFGSSDSKTSDDGKLKITLHHNRY-KNIVQAAPRVRFGQVHVYNNYY 295
>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 = 74.7 bits (182), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 70/226 (30%), Positives = 111/226 (49%), Gaps = 44/226 (19%)
Query: 235 DAVSIF-GSSNIWLDHLTLSQA-----------------HDGLIDAIQASTAITISNCHL 276
DA++I G+ ++W+DH+T+S HDG +D + S +TISN +
Sbjct: 144 DAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLI 203
Query: 277 SNHDKAILLGASDT-FTEDK-KMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNN------- 327
HDK +L+G SD+ ++DK K+ VT+ N F++ + +R P VR+G H NN
Sbjct: 204 DQHDKTMLIGHSDSNGSQDKGKLHVTLFNNVFNR-VTERAPRVRYGSIHSFNNVFKGDAK 262
Query: 328 DYNQWEMYAIGGLQGPTILSQGNRFFASNNQNAK--EVTKRMNCSPEEGKSWIWRSEGDV 385
D Y+ G ++LS+GN F +N +K +V K+ N S I+ G V
Sbjct: 263 DPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGS-------IFSDNGSV 315
Query: 386 LLNGAYFNSSG----DPKKQIQYQMDDVIKPESGTEVERITKFAGA 427
LNG+ + SG +I Y D ++P + + IT AG+
Sbjct: 316 -LNGSAVDLSGCGFSAYTSKIPYIYD--VQPMTTELAQSITDNAGS 358
>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 = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 70/226 (30%), Positives = 111/226 (49%), Gaps = 44/226 (19%)
Query: 235 DAVSIF-GSSNIWLDHLTLSQA-----------------HDGLIDAIQASTAITISNCHL 276
DA++I G+ ++W+DH+T+S HDG +D + S +TISN +
Sbjct: 144 DAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLI 203
Query: 277 SNHDKAILLGASDTFT-EDK-KMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNN------- 327
HDK +L+G +DT + +DK K+ VT+ N F++ + +R P VR+G H NN
Sbjct: 204 DQHDKTMLIGHNDTNSAQDKGKLHVTLFNNVFNR-VTERAPRVRYGSIHSFNNVFKGDAK 262
Query: 328 DYNQWEMYAIGGLQGPTILSQGNRFFASNNQNAK--EVTKRMNCSPEEGKSWIWRSEGDV 385
D Y+ G ++LS+GN F +N +K +V K+ N S I+ G V
Sbjct: 263 DPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGS-------IFSDNGSV 315
Query: 386 LLNGAYFNSSG----DPKKQIQYQMDDVIKPESGTEVERITKFAGA 427
LNG+ + SG +I Y D ++P + + IT AG+
Sbjct: 316 -LNGSAVDLSGCGFSAYTSKIPYIYD--VQPMTTELAQSITDNAGS 358
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 37/119 (31%), Positives = 62/119 (52%), Gaps = 17/119 (14%)
Query: 229 RGQSDGDAVSIFGSSN-----IWLDHLTL-----------SQAHDGLIDAIQASTAITIS 272
+G D D++S+ G+S+ IW+DH T+ + DG ID + +T+S
Sbjct: 108 QGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVS 167
Query: 273 NCHLSNHDKAILLGASDTFTEDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDYNQ 331
++ N+ K L G SD+ T++ + T NRF+ + R+P RFG +H+ NN +N
Sbjct: 168 YNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRFEN-VESRVPLQRFGLSHIYNNYFNN 225
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 37/119 (31%), Positives = 62/119 (52%), Gaps = 17/119 (14%)
Query: 229 RGQSDGDAVSIFGSSN-----IWLDHLTL-----------SQAHDGLIDAIQASTAITIS 272
+G D D++S+ G+S+ IW+DH T+ + DG ID + +T+S
Sbjct: 108 QGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVS 167
Query: 273 NCHLSNHDKAILLGASDTFTEDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDYNQ 331
++ N+ K L G SD+ T++ + T NRF+ + R+P RFG +H+ NN +N
Sbjct: 168 YNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRFEN-VESRVPLQRFGLSHIYNNYFNN 225
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 36/119 (30%), Positives = 61/119 (51%), Gaps = 17/119 (14%)
Query: 229 RGQSDGDAVSIFGSSN-----IWLDHLTL-----------SQAHDGLIDAIQASTAITIS 272
+G D D++S+ G+S+ IW+DH T+ + DG ID + +T+S
Sbjct: 108 QGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVS 167
Query: 273 NCHLSNHDKAILLGASDTFTEDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDYNQ 331
++ N+ K L G SD+ T++ + T NRF+ + R+P R G +H+ NN +N
Sbjct: 168 YNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRFEN-VESRVPLQRRGLSHIYNNYFNN 225
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 56/217 (25%), Positives = 92/217 (42%), Gaps = 31/217 (14%)
Query: 222 SVDHVGKRGQSDGDAVSIFGSS-NIWLDHLTL---------SQAHDGLIDAIQASTAITI 271
S+ HV + +G A+ + S N+W+DH S +DGL+D + + IT+
Sbjct: 111 SIHHVR---EGEGTAIEVTDDSKNVWIDHNEFYSEFPGNGDSDYYDGLVDMKRNAEYITV 167
Query: 272 SNCHLSNHDKAILLGASD--TFTEDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
S NH K +L+G +D + DK +T N F+ L R+P +R+ H+ NN +
Sbjct: 168 SWNKFENHWKTMLVGHTDNASLAPDK---ITYHHNYFNN-LNSRVPLIRYADVHMFNNYF 223
Query: 330 NQWEMYAIGGLQGPTILSQGNRFFASNNQNAKEVTKRMN-------CSPEEGKSWIWRSE 382
AI G + + N F + A T + SP G W
Sbjct: 224 KDINDTAINSRVGARVFVENNYFDNVGSGQADPTTGFIKGPVGWFYGSPSTG---YWNLR 280
Query: 383 GDVLLN--GAYFNSSGDPKKQIQYQMDDVIKPESGTE 417
G+V +N ++ NS+ + YQ+ + +S E
Sbjct: 281 GNVFVNTPNSHLNSTTNFTPPYSYQVQSATQAKSSVE 317
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 50/113 (44%), Gaps = 17/113 (15%)
Query: 230 GQSDGDAVSIFGSSNIWLDHLTLSQAH---DGL----------IDAIQASTAITISNCHL 276
G DGD + + S N+W+DH L A+ DG +D AS +T+S ++
Sbjct: 126 GAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYI 185
Query: 277 SNHDKAILLGASDTFTEDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
K L G+S + D +T N ++ + R+P R G H NN Y
Sbjct: 186 HGVKKVGLDGSS---SSDTGRNITYHHNYYND-VNARLPLQRGGLVHAYNNLY 234
>pdb|2EWE|A Chain A, Crystal Structure Of Pectate Lyase C R218k Mutant In
Complex With Pentagalacturonic Acid
Length = 353
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/113 (28%), Positives = 50/113 (44%), Gaps = 17/113 (15%)
Query: 230 GQSDGDAVSIFGSSNIWLDHLTLSQAH---DGL----------IDAIQASTAITISNCHL 276
G DGD + + S N+W+DH L A+ DG +D AS +T+S ++
Sbjct: 126 GAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYI 185
Query: 277 SNHDKAILLGASDTFTEDKKMQVTVAFNRFDKGLVQRMPCVRFGFAHVVNNDY 329
K L G+S + D +T N ++ + ++P R G H NN Y
Sbjct: 186 HGVKKVGLDGSS---SSDTGRNITYHHNYYND-VNAKLPLQRGGLVHAYNNLY 234
>pdb|1QCX|A Chain A, Pectin Lyase B
Length = 359
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 69/153 (45%), Gaps = 23/153 (15%)
Query: 234 GDAVSIFGSSNIWLDHLTLSQ-AHDGLIDAIQASTAITIS------------NCHLSNHD 280
GDA+++ S +W+DH+T ++ ++ A +TIS C+ ++
Sbjct: 153 GDAITVDDSDLVWIDHVTTARIGRQHIVLGTSADNRVTISYSLIDGRSDYSATCNGHHYW 212
Query: 281 KAILLGASDTFTEDKKMQVTVAFNRFDKGLVQRMPCVRFG-FAHVVNNDYNQWEMYAIGG 339
L G++D VT+ N F L RMP V+ H VNN ++ ++ +A
Sbjct: 213 GVYLDGSND--------MVTLKGNYF-YNLSGRMPKVQGNTLLHAVNNLFHNFDGHAFEI 263
Query: 340 LQGPTILSQGNRFFASNNQNAKEVTKRMNCSPE 372
G +L++GN F N ++ ++ SP+
Sbjct: 264 GTGGYVLAEGNVFQDVNVVVETPISGQLFSSPD 296
>pdb|1Q3S|A Chain A, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
pdb|1Q3S|B Chain B, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
pdb|1Q3S|C Chain C, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
pdb|1Q3S|D Chain D, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
pdb|1Q3S|E Chain E, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
pdb|1Q3S|F Chain F, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
pdb|1Q3S|G Chain G, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
pdb|1Q3S|H Chain H, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Formiii Crystal Complexed With Adp)
Length = 548
Score = 31.6 bits (70), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 7/94 (7%)
Query: 346 LSQGNRFFASNNQNAKEVTKRMNCSPEEGKSWIWRS-------EGDVLLNGAYFNSSGDP 398
L+ N F +N K VT + E + R+ DV+ +GA + G P
Sbjct: 355 LAGENMIFVEGCKNPKAVTILIRGGTEHVIDEVERALEDAVKVVKDVMEDGAVLPAGGAP 414
Query: 399 KKQIQYQMDDVIKPESGTEVERITKFAGALVCKP 432
+ ++ ++D+ K G E I FA AL P
Sbjct: 415 EIELAIRLDEYAKQVGGKEALAIENFADALKIIP 448
>pdb|1Q2V|A Chain A, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form)
pdb|1Q2V|B Chain B, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form)
pdb|1Q2V|C Chain C, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form)
pdb|1Q2V|D Chain D, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form)
pdb|1Q3Q|A Chain A, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Two-Point Mutant Complexed With Amp-Pnp)
pdb|1Q3Q|B Chain B, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Two-Point Mutant Complexed With Amp-Pnp)
pdb|1Q3Q|C Chain C, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Two-Point Mutant Complexed With Amp-Pnp)
pdb|1Q3Q|D Chain D, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Two-Point Mutant Complexed With Amp-Pnp)
Length = 548
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 7/94 (7%)
Query: 346 LSQGNRFFASNNQNAKEVTKRMNCSPEEGKSWIWRS-------EGDVLLNGAYFNSSGDP 398
L+ N F +N K VT + E + R+ DV+ +GA + G P
Sbjct: 355 LAGENMIFVEGCKNPKAVTILIRGGTEHVIDEVERALEDAVKVVKDVMEDGAVLPAGGAP 414
Query: 399 KKQIQYQMDDVIKPESGTEVERITKFAGALVCKP 432
+ ++ ++D+ K G E I FA AL P
Sbjct: 415 EIELAIRLDEYAKQVGGKEALAIENFADALKIIP 448
>pdb|1Q3R|A Chain A, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form Of Single Mutant)
pdb|1Q3R|B Chain B, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form Of Single Mutant)
pdb|1Q3R|C Chain C, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form Of Single Mutant)
pdb|1Q3R|D Chain D, Crystal Structure Of The Chaperonin From Thermococcus
Strain Ks-1 (Nucleotide-Free Form Of Single Mutant)
Length = 548
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 7/94 (7%)
Query: 346 LSQGNRFFASNNQNAKEVTKRMNCSPEEGKSWIWRS-------EGDVLLNGAYFNSSGDP 398
L+ N F +N K VT + E + R+ DV+ +GA + G P
Sbjct: 355 LAGENMIFVEGCKNPKAVTILIRGGTEHVIDEVERALEDAVKVVKDVMEDGAVLPAGGAP 414
Query: 399 KKQIQYQMDDVIKPESGTEVERITKFAGALVCKP 432
+ ++ ++D+ K G E I FA AL P
Sbjct: 415 EIELAIRLDEYAKQVGGKEALAIENFADALKIIP 448
>pdb|2VYC|A Chain A, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|B Chain B, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|C Chain C, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|D Chain D, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|E Chain E, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|F Chain F, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|G Chain G, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|H Chain H, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|I Chain I, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
pdb|2VYC|J Chain J, Crystal Structure Of Acid Induced Arginine Decarboxylase
From E. Coli
Length = 755
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 223 VDHVGKRGQSDGDAVSIFGSSNIWLDHLTLSQAHDGLIDAIQASTAITI--SNCHLSNHD 280
+DH G G+S+ A +FG+ W + S ++ ++ A + + NCH S
Sbjct: 201 LDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRNCHKSIEQ 260
Query: 281 KAILLGASDTF 291
+L GA +
Sbjct: 261 GLMLTGAKPVY 271
>pdb|1TWS|A Chain A, Dihydropteroate Synthetase From Bacillus Anthracis
pdb|1TWS|B Chain B, Dihydropteroate Synthetase From Bacillus Anthracis
pdb|1TWW|A Chain A, Dihydropteroate Synthetase, With Bound Substrate Analogue
Ptpp, From Bacillus Anthracis
pdb|1TWW|B Chain B, Dihydropteroate Synthetase, With Bound Substrate Analogue
Ptpp, From Bacillus Anthracis
pdb|1TWZ|A Chain A, Dihydropteroate Synthetase, With Bound Substrate Analogue
Ptp, From Bacillus Anthracis
pdb|1TWZ|B Chain B, Dihydropteroate Synthetase, With Bound Substrate Analogue
Ptp, From Bacillus Anthracis
pdb|1TX0|A Chain A, Dihydropteroate Synthetase, With Bound Product Analogue
Pteroic Acid, From Bacillus Anthracis
pdb|1TX0|B Chain B, Dihydropteroate Synthetase, With Bound Product Analogue
Pteroic Acid, From Bacillus Anthracis
pdb|1TX2|A Chain A, Dihydropteroate Synthetase, With Bound Inhibitor Manic,
From Bacillus Anthracis
pdb|1TX2|B Chain B, Dihydropteroate Synthetase, With Bound Inhibitor Manic,
From Bacillus Anthracis
pdb|3H21|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H21|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H22|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H22|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H23|A Chain A, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H23|B Chain B, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H24|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H24|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H26|A Chain A, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H26|B Chain B, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2A|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2A|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2C|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2C|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2E|A Chain A, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2E|B Chain B, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2F|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2F|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2M|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2M|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2N|A Chain A, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2N|B Chain B, Structural Studies Of Pterin-based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2O|A Chain A, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3H2O|B Chain B, Structural Studies Of Pterin-Based Inhibitors Of
Dihydropteroate Synthase
pdb|3TYA|A Chain A, Dihydropteroate Synthase In Complex With Product
pdb|3TYA|B Chain B, Dihydropteroate Synthase In Complex With Product
pdb|3TYB|A Chain A, Dihydropteroate Synthase In Complex With Phba And Dhp+
pdb|3TYB|B Chain B, Dihydropteroate Synthase In Complex With Phba And Dhp+
pdb|3TYC|A Chain A, Dihydropteroate Synthase In Complex With Dhp+
pdb|3TYC|B Chain B, Dihydropteroate Synthase In Complex With Dhp+
pdb|3TYD|A Chain A, Dihydropteroate Synthase In Complex With Ppi And Dhp+
pdb|3TYD|B Chain B, Dihydropteroate Synthase In Complex With Ppi And Dhp+
pdb|3TYE|A Chain A, Dihydropteroate Synthase In Complex With Dhp-Stz
pdb|3TYE|B Chain B, Dihydropteroate Synthase In Complex With Dhp-Stz
pdb|4D8Z|A Chain A, Crystal Structure Of B. Anthracis Dhps With Compound 24
pdb|4D8Z|B Chain B, Crystal Structure Of B. Anthracis Dhps With Compound 24
pdb|4D9P|A Chain A, Crystal Structure Of B. Anthracis Dhps With Compound 17
pdb|4D9P|B Chain B, Crystal Structure Of B. Anthracis Dhps With Compound 17
pdb|4DAI|A Chain A, Crystal Structure Of B. Anthracis Dhps With Compound 23
pdb|4DAI|B Chain B, Crystal Structure Of B. Anthracis Dhps With Compound 23
pdb|4DB7|A Chain A, Crystal Structure Of B. Anthracis Dhps With Compound 25
pdb|4DB7|B Chain B, Crystal Structure Of B. Anthracis Dhps With Compound 25
pdb|4D8A|A Chain A, Crystal Structure Of B. Anthracis Dhps With Compound 21
pdb|4D8A|B Chain B, Crystal Structure Of B. Anthracis Dhps With Compound 21
pdb|4DAF|A Chain A, Crystal Structure Of B. Anthracis Dhps With Compound 19
pdb|4DAF|B Chain B, Crystal Structure Of B. Anthracis Dhps With Compound 19
Length = 297
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 23 AHIAEVNEVWRRRAEEAMQTTEQYYDPNPVAVANHLNMKVQDLSKQAIA 71
AHI +N++W +AE + +YD + + N NM ++L IA
Sbjct: 136 AHI--INDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIA 182
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.133 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,445,433
Number of Sequences: 62578
Number of extensions: 481314
Number of successful extensions: 1081
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1036
Number of HSP's gapped (non-prelim): 24
length of query: 436
length of database: 14,973,337
effective HSP length: 102
effective length of query: 334
effective length of database: 8,590,381
effective search space: 2869187254
effective search space used: 2869187254
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)