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= 043115
(196 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 = 103 bits (258), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 58/154 (37%), Positives = 87/154 (56%), Gaps = 5/154 (3%)
Query: 48 GRGDFRTIQGAIDSVPDNNSELVFISVAPGIYREKIIVPANKPFITISGTKASHTKITWS 107
G GD++T+ A+ + P+++ I + G+YRE + VP K I G + T IT S
Sbjct: 15 GSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTIITAS 74
Query: 108 ----DGGSILDSATFTVLASHFVARSLTIQNTYGSYG-KAVALRVSADRAAFYGCRILSY 162
DG + +SAT + + F+AR +T QNT G+ +AVALRV +D +AFY C IL+Y
Sbjct: 75 KNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYRCDILAY 134
Query: 163 QHTLLDDTGNHYYSKCIIEGATDFISGNANSLFE 196
Q +L + ++ C I G DFI GNA + +
Sbjct: 135 QDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQ 168
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 90.9 bits (224), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 57/158 (36%), Positives = 82/158 (51%), Gaps = 5/158 (3%)
Query: 44 VEKYGRGDFRTIQGAIDSVPDNNSELVFISVAPGIYREKIIVPANKPFITISGTKASHTK 103
V + G GD++T+ A+ + PD + I V G Y+E + V +NK + I G T
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATT 66
Query: 104 ITWS----DGGSILDSATFTVLASHFVARSLTIQNTYG-SYGKAVALRVSADRAAFYGCR 158
IT S DG + SAT + F+ + + IQNT G + +AVALRV AD + CR
Sbjct: 67 ITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCR 126
Query: 159 ILSYQHTLLDDTGNHYYSKCIIEGATDFISGNANSLFE 196
I +YQ TL + +Y + G DFI GNA +F+
Sbjct: 127 IDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQ 164
>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 = 58.2 bits (139), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 53/172 (30%), Positives = 77/172 (44%), Gaps = 30/172 (17%)
Query: 52 FRTIQGAIDSVPDNNSELVFISVAPGIYREKIIVPANKPFITISGTKASHTKITW----- 106
F+TI AI S P ++ V + + G+Y E++ + N + + G + I
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNN--LHLKGESRNGAVIAAATAAG 74
Query: 107 ---SDGGS--ILDSATFTVLASHFVARSLTIQNTYG---------------SYGKAVALR 146
SDG S+T T+ A F A+SLTI+N + +AVAL
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 147 V--SADRAAFYGCRILSYQHTLLDDTGNHYYSKCIIEGATDFISGNANSLFE 196
V S DRA F ++ YQ TL G ++S C I G DFI G+ +LF
Sbjct: 135 VTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFN 186
>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 = 58.2 bits (139), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 52/176 (29%), Positives = 76/176 (43%), Gaps = 38/176 (21%)
Query: 52 FRTIQGAIDSVPDNNSELVFISVAPGIYREKIIVPANKPFI--------------TISGT 97
F+TI AI S P ++ V + + G+Y E++ + N +
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 98 KASHTKITWSDGGSILDSATFTVLASHFVARSLTIQNTYG---------------SYGKA 142
K+ +K W GS +T T+ A F A+SLTI+N + +A
Sbjct: 77 KSDGSK--WGTAGS----STITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQA 130
Query: 143 VALRV--SADRAAFYGCRILSYQHTLLDDTGNHYYSKCIIEGATDFISGNANSLFE 196
VAL V S DRA F ++ YQ TL G ++S C I G DFI G+ +LF
Sbjct: 131 VALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFN 186
>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 = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 53/172 (30%), Positives = 77/172 (44%), Gaps = 30/172 (17%)
Query: 52 FRTIQGAIDSVPDNNSELVFISVAPGIYREKIIVPANKPFITISGTKASHTKITW----- 106
F+TI AI S P ++ V + + G+Y E++ + N + + G + I
Sbjct: 18 FKTIADAIASAPAGSTPFVIL-IKNGVYNERLTITRNN--LHLKGESRNGAVIAAATAAG 74
Query: 107 ---SDGGS--ILDSATFTVLASHFVARSLTIQNTYG---------------SYGKAVALR 146
SDG S+T T+ A F A+SLTI+N + +AVAL
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALY 134
Query: 147 V--SADRAAFYGCRILSYQHTLLDDTGNHYYSKCIIEGATDFISGNANSLFE 196
V S DRA F ++ YQ TL G ++S C I G DFI G+ +LF
Sbjct: 135 VTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFN 186
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 46/174 (26%), Positives = 81/174 (46%), Gaps = 31/174 (17%)
Query: 51 DFRTIQGAIDSVPDNNSELVFISVAPGIYREKIIVPANKPFITISGTKASHTKITWSDGG 110
+F +I A+ S P +++ + I + G+Y E++ V + +T+ G T I +
Sbjct: 43 EFSSINAALKSAPKDDTPFI-IFLKNGVYTERLEV--ARSHVTLKGENRDGTVIGANTAA 99
Query: 111 SILD----------SATFTVLASHFVARSLTIQNTYG-----------------SYGKAV 143
+L+ S+T V A +F A +LTI+N + + A+
Sbjct: 100 GMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAVAL 159
Query: 144 ALRVSADRAAFYGCRILSYQHTLLDDTGNH-YYSKCIIEGATDFISGNANSLFE 196
L ++D+A F ++ YQ TL TG+ Y+S C I G DFI G+ ++F+
Sbjct: 160 LLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFD 213
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 51/201 (25%), Positives = 73/201 (36%), Gaps = 58/201 (28%)
Query: 54 TIQGAIDS-VPDNNSELVFISVAPGIYREKIIVPANKPFITISGT--KASHTKITWS-DG 109
TIQ A+D+ + ++ +I+V PG Y+ + VPA IT+ GT K KI S DG
Sbjct: 91 TIQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGGITLYGTGEKPIDVKIGLSLDG 150
Query: 110 G-------------------------------------SILDSATFTVLASHFVARSLTI 132
G +L SA F + ++LTI
Sbjct: 151 GMSPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLCSAVFWSQNNGLQLQNLTI 210
Query: 133 QNTYGS-----YGKAVALRVSADRAAFYGCRILSYQHTLL------------DDTGNHYY 175
+NT G AVALR D+ IL Q+T +
Sbjct: 211 ENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPRTLV 270
Query: 176 SKCIIEGATDFISGNANSLFE 196
+ IEG D +SG +F+
Sbjct: 271 TNSYIEGDVDIVSGRGAVVFD 291
>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 = 30.4 bits (67), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 95 SGTKASHTKITWSDG-GSILDSATFTVLASHFVARSLTIQNTYGSYGKAVALR--VSADR 151
+GT ASH + G G ++ + + +LA HF +L + G+ + +A+ V AD+
Sbjct: 35 TGTIASHEVVLVESGIGKVMSAMSVAILADHFQVDALINTGSAGAVAEGIAVGDVVIADK 94
Query: 152 AAFYGCRILSY 162
A++ + ++
Sbjct: 95 LAYHDVDVTAF 105
>pdb|3MMS|A Chain A, Crystal Structure Of Streptococcus Pneumoniae MtaSAH
NUCLEO Complex With 8-Aminoadenine
Length = 230
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 95 SGTKASHTKITWSDG-GSILDSATFTVLASHFVARSLTIQNTYGSYGKAVALR--VSADR 151
+GT SH + G G ++ + + +LA HF +L + G+ + +A+ V AD+
Sbjct: 35 TGTIVSHEVVLVESGIGKVMSAMSVAILAVHFQVDALINTGSAGAVAEGIAVGDVVIADK 94
Query: 152 AAFYGCRILSY 162
A++ + ++
Sbjct: 95 LAYHDVDVTAF 105
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 0.133 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,615,949
Number of Sequences: 62578
Number of extensions: 208257
Number of successful extensions: 560
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 542
Number of HSP's gapped (non-prelim): 13
length of query: 196
length of database: 14,973,337
effective HSP length: 94
effective length of query: 102
effective length of database: 9,091,005
effective search space: 927282510
effective search space used: 927282510
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: 49 (23.5 bits)