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= 017972
(363 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 = 215 bits (548), Expect = 3e-56, Method: Compositional matrix adjust.
Identities = 106/205 (51%), Positives = 142/205 (69%), Gaps = 13/205 (6%)
Query: 161 NPIDDCWRCDGNWHKNRKRLADCGIGFGRNAIGGRDGRFYVVTDPRDDDPVNPKPGTLRH 220
NPID CWR D NW +NR +LADC +GFG + +GG+ G FY VT DD+PVNP PGTLR+
Sbjct: 2 NPIDSCWRGDSNWDQNRMKLADCAVGFGSSTMGGKGGDFYTVTS-TDDNPVNPTPGTLRY 60
Query: 221 AVIQDKPLWIVFKRDMVIQLKQELIVNSFKTIDGRGANVHIANGG-CITIQFVTNVIIHG 279
++K LWI+F ++M I+LK L V KTIDGRGA+VH+ NGG C+ ++ V++VI+H
Sbjct: 61 GATREKALWIIFSQNMNIKLKMPLYVAGHKTIDGRGADVHLGNGGPCLFMRKVSHVILHS 120
Query: 280 LHVHDCKPT--GNAMVRSS----PTHYGWRTVADGDAISIFGSSHIWIDHNSLSHCADGL 333
LH+H C + G+ +V S P H DGDAI++ ++ WIDHNSLS C+DGL
Sbjct: 121 LHIHGCNTSVLGDVLVSESIGVEPVH-----AQDGDAITMRNVTNAWIDHNSLSDCSDGL 175
Query: 334 VDAVMGSTAITISNNHMTHHNEVCL 358
+D +GST ITISNNH +H++V L
Sbjct: 176 IDVTLGSTGITISNNHFFNHHKVML 200
>pdb|3ZSC|A Chain A, Catalytic Function And Substrate Recognition Of The
Pectate Lyase From Thermotoga Maritima
Length = 340
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/129 (33%), Positives = 59/129 (45%), Gaps = 12/129 (9%)
Query: 230 IVFKRDMVIQLKQELIVNSFKTIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCKPTG 289
IV +V + K+E+ V S KTI G N GG + I+ NVII +H
Sbjct: 50 IVVDGTIVFEPKREIKVLSDKTI--VGINDAKIVGGGLVIKDAQNVIIRNIHFEGF---- 103
Query: 290 NAMVRSSPTHYGWRTVADGDAISIFGSSHIWIDHNSLSHCADGLVDAVMGSTAITISNNH 349
+ P + D D I++ S HIWIDH + + DG VD S IT+S N
Sbjct: 104 --YMEDDPRGKKY----DFDYINVENSHHIWIDHITFVNGNDGAVDIKKYSNYITVSWNK 157
Query: 350 MTHHNEVCL 358
H++V L
Sbjct: 158 FVDHDKVSL 166
>pdb|1VBL|A Chain A, Structure Of The Thermostable Pectate Lyase Pl 47
Length = 416
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 47/148 (31%), Positives = 66/148 (44%), Gaps = 38/148 (25%)
Query: 239 QLKQE----LIVNSFKTIDGRGANVHIANGGCITIQFVTNVIIHGL-------HVHDCKP 287
Q KQ+ + V S +I G G + I GG + I+ V NVII + + + P
Sbjct: 119 QKKQKDRIMVYVGSNTSIIGVGKDAKIKGGGFL-IKNVDNVIIRNIEFEAPLDYFPEWDP 177
Query: 288 TGNAMVRSSPTHYGWRTVADGDAISIFGSSHIWIDHNSLS-----------------HCA 330
T + W + + D+ISI GSSHIWIDHN+ +
Sbjct: 178 TDGTLGE-------WNS--EYDSISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQH 228
Query: 331 DGLVDAVMGSTAITISNNHMTHHNEVCL 358
DG +D S ITIS N T+H++V L
Sbjct: 229 DGALDIKNSSDFITISYNVFTNHDKVTL 256
>pdb|1PCL|A Chain A, Unusual Structural Features In The Parallel Beta-Helix In
Pectate Lyases
Length = 355
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 39/144 (27%), Positives = 63/144 (43%), Gaps = 38/144 (26%)
Query: 239 QLKQELIVNSFKTIDGRGANVHIANGGCITIQFVTNVIIHGLHVH---DCKPTGNAMVRS 295
+ + ++ + S TI G G+N NG + I+ V NVI+ L++ D P
Sbjct: 71 KARSQISIPSNTTIIGVGSNGKFTNGSLV-IKGVKNVILRNLYIETPVDVAP-------- 121
Query: 296 SPTHY----GWRTVADGDAISIFGSSHIWIDHNSLSHCA-----------------DGLV 334
HY GW A+ DA I S+++W+DH ++S + DG +
Sbjct: 122 ---HYESGDGWN--AEWDAAVIDNSTNVWVDHVTISDGSFTDDKYTTKDGEKYVQHDGAL 176
Query: 335 DAVMGSTAITISNNHMTHHNEVCL 358
D GS +TIS + H++ L
Sbjct: 177 DIKKGSDYVTISYSRFELHDKTIL 200
>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 = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 52/126 (41%), Gaps = 21/126 (16%)
Query: 251 TIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCKPTGNAMVRSSPTHYGWRTVADGDA 310
TI G G N + GG I+ NVII + D + + W + D
Sbjct: 130 TIVGSGTNAKVV-GGNFQIK-SDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDN-- 185
Query: 311 ISIFGSSHIWIDHNSLSHCA-----------------DGLVDAVMGSTAITISNNHMTHH 353
I+I G +HIWIDH + + + DG DA G+ IT+S N+ H
Sbjct: 186 ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHDH 245
Query: 354 NEVCLY 359
++ ++
Sbjct: 246 DKSSIF 251
>pdb|1BN8|A Chain A, Bacillus Subtilis Pectate Lyase
Length = 420
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 52/126 (41%), Gaps = 21/126 (16%)
Query: 251 TIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCKPTGNAMVRSSPTHYGWRTVADGDA 310
TI G G N + GG I+ NVII + D + + W + D
Sbjct: 151 TIVGSGTNAKVV-GGNFQIK-SDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDN-- 206
Query: 311 ISIFGSSHIWIDHNSLSHCA-----------------DGLVDAVMGSTAITISNNHMTHH 353
I+I G +HIWIDH + + + DG DA G+ IT+S N+ H
Sbjct: 207 ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHDH 266
Query: 354 NEVCLY 359
++ ++
Sbjct: 267 DKSSIF 272
>pdb|2BSP|A Chain A, Bacillus Subtilis Pectate Lyase R279k Mutant
Length = 420
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 52/126 (41%), Gaps = 21/126 (16%)
Query: 251 TIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCKPTGNAMVRSSPTHYGWRTVADGDA 310
TI G G N + GG I+ NVII + D + + W + D
Sbjct: 151 TIVGSGTNAKVV-GGNFQIK-SDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDN-- 206
Query: 311 ISIFGSSHIWIDHNSLSHCA-----------------DGLVDAVMGSTAITISNNHMTHH 353
I+I G +HIWIDH + + + DG DA G+ IT+S N+ H
Sbjct: 207 ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHDH 266
Query: 354 NEVCLY 359
++ ++
Sbjct: 267 DKSSIF 272
>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 = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 40/147 (27%)
Query: 239 QLKQELIVNSFKTIDGRGANVHIANGGCIT--IQFVTNVIIHGLHVH---DCKPTGNAMV 293
+ + ++ + + T+ G G + NG I NVII +++ D +P
Sbjct: 78 KARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEP------ 131
Query: 294 RSSPTHY----GWRTVADGDAISIF-GSSHIWIDHNSLSHCA-----------------D 331
HY GW A+ DA++I G+ H+WIDH ++S D
Sbjct: 132 -----HYEKGDGWN--AEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHD 184
Query: 332 GLVDAVMGSTAITISNNHMTHHNEVCL 358
G +D GS +TISN+ + H++ L
Sbjct: 185 GALDIKRGSDYVTISNSLIDQHDKTML 211
>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 = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 40/147 (27%)
Query: 239 QLKQELIVNSFKTIDGRGANVHIANGGCIT--IQFVTNVIIHGLHVH---DCKPTGNAMV 293
+ + ++ + + T+ G G + NG I NVII +++ D +P
Sbjct: 78 KARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEP------ 131
Query: 294 RSSPTHY----GWRTVADGDAISIF-GSSHIWIDHNSLSHCA-----------------D 331
HY GW A+ DA++I G+ H+WIDH ++S D
Sbjct: 132 -----HYEKGDGWN--AEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHD 184
Query: 332 GLVDAVMGSTAITISNNHMTHHNEVCL 358
G +D GS +TISN+ + H++ L
Sbjct: 185 GALDIKRGSDYVTISNSLIDQHDKTML 211
>pdb|3KRG|A Chain A, Structural Insights Into Substrate Specificity And The
Anti Beta-Elimination Mechanism Of Pectate Lyase
Length = 399
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 37/129 (28%), Positives = 53/129 (41%), Gaps = 27/129 (20%)
Query: 251 TIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCK---PTGNAMVRSSPTHYGWRTVAD 307
TI G G N + GG I+ NVII + D P + SS W + D
Sbjct: 130 TIVGSGTNAKVV-GGNFQIK-SDNVIIRNIEFQDAYDYFPQWDPTAGSSGN---WASQYD 184
Query: 308 GDAISIFGSSHIWIDHNSLSHCA-----------------DGLVDAVMGSTAITISNNHM 350
I+I G +HIWIDH + + + DG DA G+ IT+S N+
Sbjct: 185 N--ITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYY 242
Query: 351 THHNEVCLY 359
H+ ++
Sbjct: 243 HDHDASSIF 251
>pdb|1QCX|A Chain A, Pectin Lyase B
Length = 359
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 48/106 (45%), Gaps = 20/106 (18%)
Query: 244 LIVNSFKTIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCKPTGNAMVRSSPTHYGWR 303
+ VNS K+I G+G I G + NVII + V D P Y W
Sbjct: 104 ITVNSNKSIVGQGTKGVIKGKGLRVVSGAKNVIIQNIAVTDINP-----------KYVW- 151
Query: 304 TVADGDAISIFGSSHIWIDHNSLSHCADGLVDAVMGSTA---ITIS 346
GDAI++ S +WIDH + + G V+G++A +TIS
Sbjct: 152 ---GGDAITVDDSDLVWIDHVTTARI--GRQHIVLGTSADNRVTIS 192
>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 = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 39/159 (24%), Positives = 69/159 (43%), Gaps = 45/159 (28%)
Query: 216 GTLRHAVIQDKPLWIVFKRDMVIQLKQELIVNSFKTIDGRGANVHIANGGCITIQFVTNV 275
GT++ Q W + + + I+ K ++ + +GAN AN G + NV
Sbjct: 50 GTIKDVCAQ----WKLPAKTVQIKNKSDVTI--------KGANGSAANFGIRVVGNAHNV 97
Query: 276 IIHGLHVHDCKPTGNAMVRSSPTHYGWRTVADGDAISIFGSS-----HIWIDHN----SL 326
II + + +++ D D+IS+ G+S IW+DHN SL
Sbjct: 98 IIQNMTI--------GLLQGGE---------DADSISLEGNSSGEPSKIWVDHNTVFASL 140
Query: 327 SHCA-------DGLVDAVMGSTAITISNNHMTHHNEVCL 358
+ C+ DG +D G +T+S N++ ++ +V L
Sbjct: 141 TKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVAL 179
>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 = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 39/159 (24%), Positives = 69/159 (43%), Gaps = 45/159 (28%)
Query: 216 GTLRHAVIQDKPLWIVFKRDMVIQLKQELIVNSFKTIDGRGANVHIANGGCITIQFVTNV 275
GT++ Q W + + + I+ K ++ + +GAN AN G + NV
Sbjct: 50 GTIKDVCAQ----WKLPAKTVQIKNKSDVTI--------KGANGSAANFGIRVVGNAHNV 97
Query: 276 IIHGLHVHDCKPTGNAMVRSSPTHYGWRTVADGDAISIFGSS-----HIWIDHN----SL 326
II + + +++ D D+IS+ G+S IW+DHN SL
Sbjct: 98 IIQNMTI--------GLLQGGE---------DADSISLEGNSSGEPSKIWVDHNTVFASL 140
Query: 327 SHCA-------DGLVDAVMGSTAITISNNHMTHHNEVCL 358
+ C+ DG +D G +T+S N++ ++ +V L
Sbjct: 141 TKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVAL 179
>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 = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 39/159 (24%), Positives = 69/159 (43%), Gaps = 45/159 (28%)
Query: 216 GTLRHAVIQDKPLWIVFKRDMVIQLKQELIVNSFKTIDGRGANVHIANGGCITIQFVTNV 275
GT++ Q W + + + I+ K ++ + +GAN AN G + NV
Sbjct: 50 GTIKDVCAQ----WKLPAKTVQIKNKSDVTI--------KGANGSAANFGIRVVGNAHNV 97
Query: 276 IIHGLHVHDCKPTGNAMVRSSPTHYGWRTVADGDAISIFGSS-----HIWIDHN----SL 326
II + + +++ D D+IS+ G+S IW+DHN SL
Sbjct: 98 IIQNMTI--------GLLQGGE---------DADSISLEGNSSGEPSKIWVDHNTVFASL 140
Query: 327 SHCA-------DGLVDAVMGSTAITISNNHMTHHNEVCL 358
+ C+ DG +D G +T+S N++ ++ +V L
Sbjct: 141 TKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVAL 179
>pdb|1IDK|A Chain A, Pectin Lyase A
Length = 359
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 51/110 (46%), Gaps = 20/110 (18%)
Query: 244 LIVNSFKTIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCKPTGNAMVRSSPTHYGWR 303
+ V S K++ G G++ I G + N+II + V D P Y W
Sbjct: 104 ITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDINP-----------KYVWG 152
Query: 304 TVADGDAISIFGSSHIWIDHNSLSHCADGLVDAVMGSTA---ITISNNHM 350
GDAI++ +WIDH + + G V+G++A ++++NN++
Sbjct: 153 ----GDAITLDDCDLVWIDHVTTARI--GRQHYVLGTSADNRVSLTNNYI 196
>pdb|1IDJ|A Chain A, Pectin Lyase A
pdb|1IDJ|B Chain B, Pectin Lyase A
Length = 359
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 51/110 (46%), Gaps = 20/110 (18%)
Query: 244 LIVNSFKTIDGRGANVHIANGGCITIQFVTNVIIHGLHVHDCKPTGNAMVRSSPTHYGWR 303
+ V S K++ G G++ I G + N+II + V D P Y W
Sbjct: 104 ITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDINP-----------KYVWG 152
Query: 304 TVADGDAISIFGSSHIWIDHNSLSHCADGLVDAVMGSTA---ITISNNHM 350
GDAI++ +WIDH + + G V+G++A ++++NN++
Sbjct: 153 ----GDAITLDDCDLVWIDHVTTARI--GRQHYVLGTSADNRVSLTNNYI 196
>pdb|2EWE|A Chain A, Crystal Structure Of Pectate Lyase C R218k Mutant In
Complex With Pentagalacturonic Acid
Length = 353
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 13/65 (20%)
Query: 307 DGDAISIFGSSHIWIDHNSL---SHCADGL----------VDAVMGSTAITISNNHMTHH 353
DGD I + S ++W+DHN L +H DG VD S +T+S N++
Sbjct: 129 DGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGV 188
Query: 354 NEVCL 358
+V L
Sbjct: 189 KKVGL 193
>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 = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 13/65 (20%)
Query: 307 DGDAISIFGSSHIWIDHNSL---SHCADGL----------VDAVMGSTAITISNNHMTHH 353
DGD I + S ++W+DHN L +H DG VD S +T+S N++
Sbjct: 129 DGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGV 188
Query: 354 NEVCL 358
+V L
Sbjct: 189 KKVGL 193
>pdb|1RK2|A Chain A, E. Coli Ribokinase Complexed With Ribose And Adp, Solved
In Space Group P212121
pdb|1RK2|B Chain B, E. Coli Ribokinase Complexed With Ribose And Adp, Solved
In Space Group P212121
pdb|1RK2|C Chain C, E. Coli Ribokinase Complexed With Ribose And Adp, Solved
In Space Group P212121
pdb|1RK2|D Chain D, E. Coli Ribokinase Complexed With Ribose And Adp, Solved
In Space Group P212121
pdb|1RKA|A Chain A, The Apo Form Of E. Coli Ribokinase
pdb|1RKS|A Chain A, E. Coli Ribokinase In Complex With D-Ribose
pdb|1GQT|A Chain A, Activation Of Ribokinase By Monovalent Cations
pdb|1GQT|B Chain B, Activation Of Ribokinase By Monovalent Cations
pdb|1GQT|C Chain C, Activation Of Ribokinase By Monovalent Cations
pdb|1GQT|D Chain D, Activation Of Ribokinase By Monovalent Cations
pdb|1RKD|A Chain A, E. Coli Ribokinase Complexed With Ribose And Adp
Length = 309
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 103 MKAESSMNSTMAA-----KAEVVAEALSKHAVDNPDEIASMVEMSTRNSTERRKL 152
M+ ES + S MAA + + + A + PDE+ ++V++ T N TE KL
Sbjct: 140 MQLESPLESVMAAAKIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKL 194
>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 = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 10/63 (15%)
Query: 306 ADGDAISIFG-SSHIWIDHNSL---------SHCADGLVDAVMGSTAITISNNHMTHHNE 355
+G AI + S ++WIDHN S DGLVD + IT+S N +H +
Sbjct: 118 GEGTAIEVTDDSKNVWIDHNEFYSEFPGNGDSDYYDGLVDMKRNAEYITVSWNKFENHWK 177
Query: 356 VCL 358
L
Sbjct: 178 TML 180
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 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,559,267
Number of Sequences: 62578
Number of extensions: 416405
Number of successful extensions: 1086
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1065
Number of HSP's gapped (non-prelim): 24
length of query: 363
length of database: 14,973,337
effective HSP length: 100
effective length of query: 263
effective length of database: 8,715,537
effective search space: 2292186231
effective search space used: 2292186231
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: 52 (24.6 bits)