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= 042845
(327 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 = 176 bits (445), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 104/301 (34%), Positives = 150/301 (49%), Gaps = 20/301 (6%)
Query: 32 GRGDFRTIQEAIDSVPANNSELVFISVAPGIYKEKIIVPANKPFITISGTKASHTKITWS 91
G GD++T+ EA+ + P ++ I + G+Y+E + VP K I G + T IT S
Sbjct: 15 GSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTIITAS 74
Query: 92 ----DGGSILDSATLTVLASHFVARSLTIQNTYGSFG-KAVALRVSADKAAFYGCRILSY 146
DG + +SAT+ + + F+AR +T QNT G+ +AVALRV +D +AFY C IL+Y
Sbjct: 75 KNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYRCDILAY 134
Query: 147 QHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSLSTWGGA---ITAQKRVSSE 203
Q +L + ++ C+I G DFI GNA + C IH+ G +TAQ R
Sbjct: 135 QDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQGRTDPN 194
Query: 204 ENTGFTFLDCKISGVG---------KAVLGRPWGAYSRVVYALTYMSDVIVPQGWNDLND 254
+NTG +I LGRPW YSR V + +++VI P GW +
Sbjct: 195 QNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAGWFPWDG 254
Query: 255 HAKHNKLYYGEYRCSGPGADRSKRIAWSN---SLSDVEASTFLSKDLTGRGTWLRNAALK 311
+ + LYYGEY+ +G GA S R+ W S EA F G+WL+
Sbjct: 255 NFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGGSWLKATTFP 314
Query: 312 F 312
F
Sbjct: 315 F 315
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 162 bits (410), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 105/307 (34%), Positives = 150/307 (48%), Gaps = 20/307 (6%)
Query: 28 VEKYGRGDFRTIQEAIDSVPANNSELVFISVAPGIYKEKIIVPANKPFITISGTKASHTK 87
V + G GD++T+ EA+ + P + I V G YKE + V +NK + I G T
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATT 66
Query: 88 ITWS----DGGSILDSATLTVLASHFVARSLTIQNTYG-SFGKAVALRVSADKAAFYGCR 142
IT S DG + SATL + F+ + + IQNT G + +AVALRV AD + CR
Sbjct: 67 ITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCR 126
Query: 143 ILSYQHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSLST---WGGAITAQKR 199
I +YQ TL + +Y Y+ G DFI GNA F++C + + +TAQ R
Sbjct: 127 IDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGR 186
Query: 200 VSSEENTGFTFLDCKISGVG---------KAVLGRPWGAYSRVVYALTYMSDVIVPQGWN 250
+ TG + C I LGRPW YSR V +Y+ +I P GW
Sbjct: 187 TDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWA 246
Query: 251 DLNDHAKHNKLYYGEYRCSGPGADRSKRIAWS--NSLSD-VEASTFLSKDLTGRGTWLRN 307
+ + LYYGE+ +GPGA SKR+ W + ++D +A F L G+WLR+
Sbjct: 247 EWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRS 306
Query: 308 AALKFKD 314
+ + 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 = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 83/325 (25%), Positives = 133/325 (40%), Gaps = 67/325 (20%)
Query: 36 FRTIQEAIDSVPANNSELVFISVAPGIYKEKIIVPANKPFI------TISGTKASHTKIT 89
F+TI +AI S PA ++ V + + G+Y E++ + N + A+
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 90 WSDGGS--ILDSATLTVLASHFVARSLTIQNTYG---------------SFGKAVALRV- 131
SDG S+T+T+ A F A+SLTI+N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 132 -SADKAAFYGCRILSYQHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSL--- 187
S D+A F ++ YQ TL G ++S C I G DFI G+ + F C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 188 ----STWGGAITAQKRVSSEENTGFTFLDCKISGVGKAV------LGRPW---------- 227
G +TA + + G + ++ +V LGRPW
Sbjct: 197 DVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 228 ----GAYSRVVYALTYMSDVIVPQGWNDLNDHAKH-NKLYYG-------EYRCSGPGADR 275
A + V+ T M + I GW+ ++ K+ N +++ EY+ G GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATV 313
Query: 276 SKRIAWSNSLSDVEASTFLSKDLTG 300
SK L+D +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 = 70.1 bits (170), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 83/325 (25%), Positives = 133/325 (40%), Gaps = 67/325 (20%)
Query: 36 FRTIQEAIDSVPANNSELVFISVAPGIYKEKIIVPANKPFI------TISGTKASHTKIT 89
F+TI +AI S PA ++ V + + G+Y E++ + N + A+
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 90 WSDGGS--ILDSATLTVLASHFVARSLTIQNTYG---------------SFGKAVALRV- 131
SDG S+T+T+ A F A+SLTI+N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 132 -SADKAAFYGCRILSYQHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSL--- 187
S D+A F ++ YQ TL G ++S C I G DFI G+ + F C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 188 ----STWGGAITAQKRVSSEENTGFTFLDCKISGVGKAV------LGRPW---------- 227
G +TA + + G + ++ +V LGRPW
Sbjct: 197 DVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 228 ----GAYSRVVYALTYMSDVIVPQGWNDLNDHAKH-NKLYYG-------EYRCSGPGADR 275
A + V+ T M + I GW+ ++ K+ N +++ EY+ G GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATV 313
Query: 276 SKRIAWSNSLSDVEASTFLSKDLTG 300
SK L+D +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 = 70.1 bits (170), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 83/325 (25%), Positives = 133/325 (40%), Gaps = 67/325 (20%)
Query: 36 FRTIQEAIDSVPANNSELVFISVAPGIYKEKIIVPANKPFI------TISGTKASHTKIT 89
F+TI +AI S PA ++ V + + G+Y E++ + N + A+
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 90 WSDGGS--ILDSATLTVLASHFVARSLTIQNTYG---------------SFGKAVALRV- 131
SDG S+T+T+ A F A+SLTI+N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 132 -SADKAAFYGCRILSYQHTLLDDTGNHYYSKCYIEGATDFISGNANSFFERCLIHSL--- 187
S D+A F ++ YQ TL G ++S C I G DFI G+ + F C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 188 ----STWGGAITAQKRVSSEENTGFTFLDCKISGVGKAV------LGRPW---------- 227
G +TA + + G + ++ +V LGRPW
Sbjct: 197 DVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 228 ----GAYSRVVYALTYMSDVIVPQGWNDLNDHAKH-NKLYYG-------EYRCSGPGADR 275
A + V+ T M + I GW+ ++ K+ N +++ EY+ G GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAV 313
Query: 276 SKRIAWSNSLSDVEASTFLSKDLTG 300
SK L+D +A+ + + G
Sbjct: 314 SKD---RRQLTDAQAAEYTQSKVLG 335
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 79/299 (26%), Positives = 130/299 (43%), Gaps = 66/299 (22%)
Query: 35 DFRTIQEAIDSVPANNSELVFISVAPGIYKEKIIVPANKPFITISGTKASHTKITWSDGG 94
+F +I A+ S P +++ + I + G+Y E++ V + +T+ G T I +
Sbjct: 43 EFSSINAALKSAPKDDTPFI-IFLKNGVYTERLEV--ARSHVTLKGENRDGTVIGANTAA 99
Query: 95 SILD----------SATLTVLASHFVARSLTIQNTYGSFG---------------KAVAL 129
+L+ S+T+ V A +F A +LTI+N + +AVAL
Sbjct: 100 GMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAVAL 159
Query: 130 RVS--ADKAAFYGCRILSYQHTLLDDTGNH-YYSKCYIEGATDFISGNANSFFERCLI-- 184
++ +DKA F ++ YQ TL TG+ Y+S C I G DFI G+ + F+ C I
Sbjct: 160 LLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCNIVA 219
Query: 185 ---HSLSTWGGAITAQKRVSSEENTGFTFLDCKIS---GV--GKAVLGRPW--------- 227
+ G ITA +++ G F++ +++ GV LGRPW
Sbjct: 220 RDRSDIEPPYGYITAPSTLTTSP-YGLIFINSRLTKEPGVPANSFALGRPWHPTTTFADG 278
Query: 228 -----GAYSRVVYALTYMSDVIVPQGWNDLNDHAKH-NKLY-------YGEYRCSGPGA 273
A + 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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 51/201 (25%), Positives = 72/201 (35%), Gaps = 58/201 (28%)
Query: 38 TIQEAIDS-VPANNSELVFISVAPGIYKEKIIVPANKPFITISGT--KASHTKITWS-DG 93
TIQ A+D+ + ++ +I+V PG Y+ + VPA IT+ GT K KI S DG
Sbjct: 91 TIQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGGITLYGTGEKPIDVKIGLSLDG 150
Query: 94 G-------------------------------------SILDSATLTVLASHFVARSLTI 116
G +L SA + ++LTI
Sbjct: 151 GMSPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLCSAVFWSQNNGLQLQNLTI 210
Query: 117 QNTYGSF-----GKAVALRVSADKAAFYGCRILSYQHTLL------------DDTGNHYY 159
+NT G AVALR D+ IL Q+T +
Sbjct: 211 ENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPRTLV 270
Query: 160 SKCYIEGATDFISGNANSFFE 180
+ YIEG D +SG F+
Sbjct: 271 TNSYIEGDVDIVSGRGAVVFD 291
>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 = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 244 IVPQGWNDLNDHAKHNKLYYGEYRCSGPGADRSKRIAWSNSLSDV 288
+ P+G L+ N+L Y EYR PG+D+ +RI+W + S +
Sbjct: 91 LCPKGAGLLDYVNSENRLRYPEYRA--PGSDKWQRISWEEAFSRI 133
>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 = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 79 SGTKASHTKITWSDG-GSILDSATLTVLASHFVARSLTIQNTYGSFGKAVAL--RVSADK 135
+GT ASH + G G ++ + ++ +LA HF +L + G+ + +A+ V ADK
Sbjct: 35 TGTIASHEVVLVESGIGKVMSAMSVAILADHFQVDALINTGSAGAVAEGIAVGDVVIADK 94
Query: 136 AAFYGCRILSY 146
A++ + ++
Sbjct: 95 LAYHDVDVTAF 105
>pdb|2QX2|A Chain A, Structure Of The C-Terminal Domain Of Sex Pheromone
Staph-Cam373 Precursor From Staphylococcus Aureus
Length = 344
Score = 31.6 bits (70), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 62/144 (43%), Gaps = 23/144 (15%)
Query: 50 NSELVFISVAPGIYK---EKIIVPANKPFITISGTKASHTKIT-W---SDGGSILDSATL 102
N +L I + IYK E I P FIT + + S TK+ W ++ ++L S+T
Sbjct: 180 NDDLKDIPIHFAIYKQSSEDSITPGE--FITQATAEKSQTKLNEWHNINEKSALLPSSTA 237
Query: 103 ----TVLASHFVARSLTIQNTYGSFGKAVALRVSADKAAFYGCRILSYQHTLLDDTGNHY 158
L ++F + +Q+ + +F +AV DK L+ D Y
Sbjct: 238 ADYDENLNNNFKQFNDNLQSYFSNFTQAVGKVKFVDKKP----------QRLVVDLPIDY 287
Query: 159 YSKCYIEGATDFISGNANSFFERC 182
Y + G T +++ AN +F++
Sbjct: 288 YGQAETIGITQYVTEQANKYFDKI 311
>pdb|3MMS|A Chain A, Crystal Structure Of Streptococcus Pneumoniae MtaSAH
NUCLEO Complex With 8-Aminoadenine
Length = 230
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 79 SGTKASHTKITWSDG-GSILDSATLTVLASHFVARSLTIQNTYGSFGKAVAL--RVSADK 135
+GT SH + G G ++ + ++ +LA HF +L + G+ + +A+ V ADK
Sbjct: 35 TGTIVSHEVVLVESGIGKVMSAMSVAILAVHFQVDALINTGSAGAVAEGIAVGDVVIADK 94
Query: 136 AAFYGCRILSY 146
A++ + ++
Sbjct: 95 LAYHDVDVTAF 105
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 19 DISTAVLIRVEKYGRGDFRTIQEAIDS-VPANNSELVFISVAPGIYKEKIIVPANKPF 75
D S ++ +K DF+TI E I S +P + L+F + P KE ++ +KP+
Sbjct: 163 DCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPY 220
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
0.319 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,058,237
Number of Sequences: 62578
Number of extensions: 416126
Number of successful extensions: 1130
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1097
Number of HSP's gapped (non-prelim): 24
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)