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= 038331
(321 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GQ8|A Chain A, Pectin Methylesterase From Carrot
Length = 319
Score = 172 bits (436), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 105/301 (34%), Positives = 150/301 (49%), Gaps = 20/301 (6%)
Query: 20 IRVEKYGRGDFRTIQEAIDSVPANNAELVFISVAPGIYREKIIVPANKPFITISGTRASH 79
+ V G GD++T+ EA+ + P ++ I + G+YRE + VP K I G +
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTS 68
Query: 80 TKITWS----DGGSILDSATLTVLASHFIARSLTIQNTYGSYG-KAVALRVSADRAAFYG 134
T IT S DG + +SAT+ + + F+AR +T QNT G+ +AVALRV +D +AFY
Sbjct: 69 TIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYR 128
Query: 135 CRILSYNHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSLSTWGGA---ITAQ 191
C IL+Y +L + ++ C+I G DFI GNA + C IH+ G +TAQ
Sbjct: 129 CDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQ 188
Query: 192 KRVSSQENTGFTFLDCKISGVG---------KAVLGRTWGPYSRVVYALTYMSDVIVPQG 242
R +NTG +I LGR W YSR V + +++VI P G
Sbjct: 189 GRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAG 248
Query: 243 WNDLNDHAKHNKLYYGEYRCSGPGADGSKRVAWSN---SLSDAEASMFLSKDLTGGGAWL 299
W + + + LYYGEY+ +G GA S RV W S EA F GG+WL
Sbjct: 249 WFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGGSWL 308
Query: 300 R 300
+
Sbjct: 309 K 309
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 158 bits (400), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 106/307 (34%), Positives = 149/307 (48%), Gaps = 20/307 (6%)
Query: 22 VEKYGRGDFRTIQEAIDSVPANNAELVFISVAPGIYREKIIVPANKPFITISGTRASHTK 81
V + G GD++T+ EA+ + P + I V G Y+E + V +NK + I G T
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATT 66
Query: 82 ITWS----DGGSILDSATLTVLASHFIARSLTIQNTYG-SYGKAVALRVSADRAAFYGCR 136
IT S DG + SATL + FI + + IQNT G + +AVALRV AD + CR
Sbjct: 67 ITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCR 126
Query: 137 ILSYNHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSLST---WGGAITAQKR 193
I +Y TL + +Y Y+ G DFI GNA F++C + + +TAQ R
Sbjct: 127 IDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGR 186
Query: 194 VSSQENTGFTFLDCKISGVG---------KAVLGRTWGPYSRVVYALTYMSDVIVPQGWN 244
+ TG + C I LGR W YSR V +Y+ +I P GW
Sbjct: 187 TDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWA 246
Query: 245 DLNDHAKHNKLYYGEYRCSGPGADGSKRVAWS--NSLSD-AEASMFLSKDLTGGGAWLRN 301
+ + LYYGE+ +GPGA SKRV W + ++D A+A F L GG+WLR+
Sbjct: 247 EWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRS 306
Query: 302 AALKLKD 308
+ D
Sbjct: 307 TGVAYVD 313
>pdb|2NTB|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide V
pdb|2NTB|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide V
pdb|2NTP|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vi
pdb|2NTP|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vi
pdb|2NTQ|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vii
pdb|2NTQ|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vii
Length = 342
Score = 68.6 bits (166), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 84/325 (25%), Positives = 133/325 (40%), Gaps = 67/325 (20%)
Query: 30 FRTIQEAIDSVPANNAELVFISVAPGIYREKIIVPANKPFI------TISGTRASHTKIT 83
F+TI +AI S PA + V + + G+Y E++ + N + A+
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 84 WSDGGS--ILDSATLTVLASHFIARSLTIQNTYG---------------SYGKAVALRV- 125
SDG S+T+T+ A F A+SLTI+N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 126 -SADRAAFYGCRILSYNHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSL--- 181
S DRA F ++ Y TL G ++S C I G DFI G+ + F C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 182 ----STWGGAITAQKRVSSQENTGFTFLDCKISGVGKAV------LGRTWGPYS------ 225
G +TA +Q+ G + ++ +V LGR W P +
Sbjct: 197 DVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 226 --------RVVYALTYMSDVIVPQGWNDLNDHAKH-NKLYYG-------EYRCSGPGADG 269
+ V+ T M + I GW+ ++ K+ N +++ EY+ G GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATV 313
Query: 270 SKRVAWSNSLSDAEASMFLSKDLTG 294
SK L+DA+A+ + + G
Sbjct: 314 SKD---RRQLTDAQAAEYTQSKVLG 335
>pdb|2NSP|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide I
pdb|2NSP|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide I
pdb|2NST|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Ii
pdb|2NST|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Ii
pdb|2NT6|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iii
pdb|2NT6|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iii
pdb|2NT9|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iv
pdb|2NT9|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iv
Length = 342
Score = 68.2 bits (165), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 84/325 (25%), Positives = 133/325 (40%), Gaps = 67/325 (20%)
Query: 30 FRTIQEAIDSVPANNAELVFISVAPGIYREKIIVPANKPFI------TISGTRASHTKIT 83
F+TI +AI S PA + V + + G+Y E++ + N + A+
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 84 WSDGGS--ILDSATLTVLASHFIARSLTIQNTYG---------------SYGKAVALRV- 125
SDG S+T+T+ A F A+SLTI+N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 126 -SADRAAFYGCRILSYNHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSL--- 181
S DRA F ++ Y TL G ++S C I G DFI G+ + F C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 182 ----STWGGAITAQKRVSSQENTGFTFLDCKISGVGKAV------LGRTWGPYS------ 225
G +TA +Q+ G + ++ +V LGR W P +
Sbjct: 197 DVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 226 --------RVVYALTYMSDVIVPQGWNDLNDHAKH-NKLYYG-------EYRCSGPGADG 269
+ V+ T M + I GW+ ++ K+ N +++ EY+ G GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATV 313
Query: 270 SKRVAWSNSLSDAEASMFLSKDLTG 294
SK L+DA+A+ + + G
Sbjct: 314 SKD---RRQLTDAQAAEYTQSKVLG 335
>pdb|1QJV|A Chain A, Pectin Methylesterase Pema From Erwinia Chrysanthemi
pdb|1QJV|B Chain B, Pectin Methylesterase Pema From Erwinia Chrysanthemi
Length = 342
Score = 68.2 bits (165), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 84/325 (25%), Positives = 133/325 (40%), Gaps = 67/325 (20%)
Query: 30 FRTIQEAIDSVPANNAELVFISVAPGIYREKIIVPANKPFI------TISGTRASHTKIT 83
F+TI +AI S PA + V + + G+Y E++ + N + A+
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 84 WSDGGS--ILDSATLTVLASHFIARSLTIQNTYG---------------SYGKAVALRV- 125
SDG S+T+T+ A F A+SLTI+N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 126 -SADRAAFYGCRILSYNHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSL--- 181
S DRA F ++ Y TL G ++S C I G DFI G+ + F C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 182 ----STWGGAITAQKRVSSQENTGFTFLDCKISGVGKAV------LGRTWGPYS------ 225
G +TA +Q+ G + ++ +V LGR W P +
Sbjct: 197 DVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 226 --------RVVYALTYMSDVIVPQGWNDLNDHAKH-NKLYYG-------EYRCSGPGADG 269
+ V+ T M + I GW+ ++ K+ N +++ EY+ G GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAV 313
Query: 270 SKRVAWSNSLSDAEASMFLSKDLTG 294
SK L+DA+A+ + + G
Sbjct: 314 SKD---RRQLTDAQAAEYTQSKVLG 335
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 64.3 bits (155), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 76/299 (25%), Positives = 128/299 (42%), Gaps = 66/299 (22%)
Query: 29 DFRTIQEAIDSVPANNAELVFISVAPGIYREKIIVPANKPFITISGTRASHTKITWSDGG 88
+F +I A+ S P ++ + I + G+Y E++ V + +T+ G T I +
Sbjct: 43 EFSSINAALKSAPKDDTPFI-IFLKNGVYTERLEV--ARSHVTLKGENRDGTVIGANTAA 99
Query: 89 SILD----------SATLTVLASHFIARSLTIQNTYGSYG---------------KAVAL 123
+L+ S+T+ V A +F A +LTI+N + +AVAL
Sbjct: 100 GMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAVAL 159
Query: 124 RVS--ADRAAFYGCRILSYNHTLLDDTGNH-YYSKCYIEGATDFISGNANSFFERCLI-- 178
++ +D+A F ++ Y TL TG+ Y+S C I G DFI G+ + F+ C I
Sbjct: 160 LLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCNIVA 219
Query: 179 ---HSLSTWGGAITAQKRVSSQENTGFTFLDCKIS---GV--GKAVLGRTWGPYS----- 225
+ G ITA +++ G F++ +++ GV LGR W P +
Sbjct: 220 RDRSDIEPPYGYITAPSTLTTSP-YGLIFINSRLTKEPGVPANSFALGRPWHPTTTFADG 278
Query: 226 ---------RVVYALTYMSDVIVPQGWNDLNDHAKH-NKLY-------YGEYRCSGPGA 267
+ V+ T M D I GW+ ++ K K++ + E GPGA
Sbjct: 279 RYADPAAIGQSVFINTTMDDHIY--GWDKMSGKDKQGEKIWFYPQDSRFFEANSQGPGA 335
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 59/252 (23%), Positives = 92/252 (36%), Gaps = 64/252 (25%)
Query: 32 TIQEAIDS-VPANNAELVFISVAPGIYREKIIVPANKPFITISGT--RASHTKITWS-DG 87
TIQ A+D+ + + +I+V PG Y+ + VPA IT+ GT + KI S DG
Sbjct: 91 TIQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGGITLYGTGEKPIDVKIGLSLDG 150
Query: 88 G-------------------------------------SILDSATLTVLASHFIARSLTI 110
G +L SA + ++LTI
Sbjct: 151 GMSPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLCSAVFWSQNNGLQLQNLTI 210
Query: 111 QNTYGS-----YGKAVALRVSADRAAFYGCRILSYNHTLL------------DDTGNHYY 153
+NT G AVALR D+ IL +T +
Sbjct: 211 ENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPRTLV 270
Query: 154 SKCYIEGATDFISGNANSFFERC---LIHSLSTWGGAITAQKRVSSQENTGFTFLDCKIS 210
+ YIEG D +SG F+ +++S + + A +S+ GF ++ + +
Sbjct: 271 TNSYIEGDVDIVSGRGAVVFDNTEFRVVNSRTQQEAYVFAPATLSNIY-YGFLAVNSRFN 329
Query: 211 GVGKAV--LGRT 220
G V LGR+
Sbjct: 330 AFGDGVAQLGRS 341
>pdb|1ZOS|A Chain A, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|B Chain B, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|C Chain C, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|D Chain D, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|E Chain E, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
pdb|1ZOS|F Chain F, Structure Of 5'-MethylthionadenosineS-Adenosylhomocysteine
Nucleosidase From S. Pneumoniae With A Transition-State
Inhibitor Mt-Imma
Length = 230
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 22/97 (22%), Positives = 45/97 (46%), Gaps = 7/97 (7%)
Query: 73 SGTRASHTKITWSDG-GSILDSATLTVLASHFIARSLTIQNTYGSYGKAVAL--RVSADR 129
+GT ASH + G G ++ + ++ +LA HF +L + G+ + +A+ V AD+
Sbjct: 35 TGTIASHEVVLVESGIGKVMSAMSVAILADHFQVDALINTGSAGAVAEGIAVGDVVIADK 94
Query: 130 AAFYGCRILSYNHTLLDDTGNHYYSKCYIEGATDFIS 166
A++ + ++ + G Y E F++
Sbjct: 95 LAYHDVDVTAFGYAY----GQMAQQPLYFESDKTFVA 127
>pdb|1KQF|A Chain A, Formate Dehydrogenase N From E. Coli
pdb|1KQG|A Chain A, Formate Dehydrogenase N From E. Coli
Length = 1015
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 238 IVPQGWNDLNDHAKHNKLYYGEYRCSGPGADGSKRVAWSNSLSDAEASMFLSKD 291
+ P+G L+ N+L Y EYR PG+D +R++W + S M +D
Sbjct: 91 LCPKGAGLLDYVNSENRLRYPEYRA--PGSDKWQRISWEEAFSRIAKLMKADRD 142
>pdb|3MMS|A Chain A, Crystal Structure Of Streptococcus Pneumoniae MtaSAH
NUCLEO Complex With 8-Aminoadenine
Length = 230
Score = 30.8 bits (68), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 7/97 (7%)
Query: 73 SGTRASHTKITWSDG-GSILDSATLTVLASHFIARSLTIQNTYGSYGKAVAL--RVSADR 129
+GT SH + G G ++ + ++ +LA HF +L + G+ + +A+ V AD+
Sbjct: 35 TGTIVSHEVVLVESGIGKVMSAMSVAILAVHFQVDALINTGSAGAVAEGIAVGDVVIADK 94
Query: 130 AAFYGCRILSYNHTLLDDTGNHYYSKCYIEGATDFIS 166
A++ + ++ + G Y E F++
Sbjct: 95 LAYHDVDVTAFGYA----YGQMAQQPLYFESDKTFVA 127
>pdb|2W9M|A Chain A, Structure Of Family X Dna Polymerase From Deinococcus
Radiodurans
pdb|2W9M|B Chain B, Structure Of Family X Dna Polymerase From Deinococcus
Radiodurans
Length = 578
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 12/77 (15%)
Query: 38 DSVPANNAELVF----ISVAPGIYREK------IIVPANKPFITISGTRAS-HTKITWSD 86
+ +P +VF + P YRE +P +T+ R HT TWSD
Sbjct: 280 EVLPTPTEAVVFHALDLPFRPAEYREPEHDDLWQTLPDPAELVTVGDLRGMIHTHSTWSD 339
Query: 87 GG-SILDSATLTVLASH 102
GG SI + A T+ H
Sbjct: 340 GGASIREMAEATLTLGH 356
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 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,182,121
Number of Sequences: 62578
Number of extensions: 423063
Number of successful extensions: 923
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 896
Number of HSP's gapped (non-prelim): 16
length of query: 321
length of database: 14,973,337
effective HSP length: 99
effective length of query: 222
effective length of database: 8,778,115
effective search space: 1948741530
effective search space used: 1948741530
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: 51 (24.3 bits)