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= 021844
(306 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 = 159 bits (402), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 103/307 (33%), Positives = 146/307 (47%), Gaps = 40/307 (13%)
Query: 6 VTVAQDGTGDYRTVQEAIDRVPLCNTRRTLIRISPGVYRQPVYVPKTKNLITLAGLCPEN 65
V VA DG+GDY+TV EA+ P + R +IRI GVYR+ V VPK K I G +
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTS 68
Query: 66 TVLTWNNTATKIEHHQAARVIGTGTFGCGSVIVEGEDFVAENITFENSAPEGSGQAVAIR 125
T++T + G+ TF +V G F+A +ITF+N+A QAVA+R
Sbjct: 69 TIITASKNVQD----------GSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALR 118
Query: 126 VTADRCAFYNCRFLGW----------QYLKDCYIEGSVDFIFGNSTALIEHCHIHCKSQG 175
V +D AFY C L + Q+ +C+I G+VDFIFGN+ +++ C IH + G
Sbjct: 119 VGSDLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPG 178
Query: 176 -----FITAQSRKSSQETTGYVFLRCVITGNGGTGYI---------YLGRPWGPFGRVVF 221
+TAQ R + TG V + I G T + YLGRPW + R V
Sbjct: 179 SGQKNMVTAQGRTDPNQNTGIVIQKSRI---GATSDLQPVQSSFPTYLGRPWKEYSRTVV 235
Query: 222 AFTYMDQCIRHVGWHNWGKVENERSACFYEYRCFGPGSCPAKRETWARELL---DEEAEQ 278
+ + I GW W + + EY+ G G+ + R TW + EA+
Sbjct: 236 MQSSITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQG 295
Query: 279 FLMHNFI 285
F +FI
Sbjct: 296 FTPGSFI 302
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 132 bits (331), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 83/281 (29%), Positives = 128/281 (45%), Gaps = 31/281 (11%)
Query: 8 VAQDGTGDYRTVQEAIDRVPLCNTRRTLIRISPGVYRQPVYVPKTKNLITLAGLCPENTV 67
VAQDGTGDY+T+ EA+ P + R +I + G Y++ V V K + + G T
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATT 66
Query: 68 LTWNNTATKIEHHQAARVIGTGTFGCGSVIVEGEDFVAENITFENSAPEGSGQAVAIRVT 127
+T + V G+ TF ++ G+ F+ ++I +N+A QAVA+RV
Sbjct: 67 ITGSLNV----------VDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVG 116
Query: 128 ADRCAFYNCRFLGWQ----------YLKDCYIEGSVDFIFGNSTALIEHCHIHCKS---- 173
AD CR +Q + +D Y+ G+VDFIFGN+ + + C + +
Sbjct: 117 ADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKY 176
Query: 174 -QGFITAQSRKSSQETTGYVFLRCVITGNGGTGYI------YLGRPWGPFGRVVFAFTYM 226
Q +TAQ R + TG C I + + YLGRPW + R V +Y+
Sbjct: 177 QQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYL 236
Query: 227 DQCIRHVGWHNWGKVENERSACFYEYRCFGPGSCPAKRETW 267
I GW W ++ + E+ GPG+ +KR W
Sbjct: 237 GGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKW 277
>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 = 84.7 bits (208), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 91/343 (26%), Positives = 146/343 (42%), Gaps = 73/343 (21%)
Query: 3 SCVVTVAQDGTGDYRTVQEAIDRVPLCNTRRTLIRISPGVYRQPVYVPKTKNLITLAGLC 62
+ VV+ + ++T+ +AI P +T +I I GVY + + + T+N + L G
Sbjct: 5 NAVVSKSSSDGKTFKTIADAIASAPAGSTP-FVILIKNGVYNERLTI--TRNNLHLKGES 61
Query: 63 PENTVLTWNNTATKIEHHQAARVIGTGTFGCGSVIVEGEDFVAENITFEN---------- 112
V+ A ++ + GT G ++ + +DF A+++T N
Sbjct: 62 RNGAVIAAATAAGTLKSDGSKW----GTAGSSTITISAKDFSAQSLTIRNDFDFPANQAK 117
Query: 113 ----SAPEGSGQAVAIRVT--ADRCAFYNCRFLGWQ----------YLKDCYIEGSVDFI 156
S+ QAVA+ VT DR F + +G+Q + DC I G+VDFI
Sbjct: 118 SDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFI 177
Query: 157 FGNSTALIEHCHI------HCKS---QGFITAQSRKSSQETTGYVFL--RCVITGNGGTG 205
FG+ TAL +C + KS G++TA S +Q+ G V R + +
Sbjct: 178 FGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPA 236
Query: 206 YIY-LGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNW-GKVENERS--- 246
Y LGRPW P G+ VF T MD I GW GK +N +
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 247 ----ACFYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI 285
+ F+EY+ +G G+ +K R+L D +A ++ +
Sbjct: 295 NPEDSRFFEYKSYGAGAAVSKDR---RQLTDAQAAEYTQSKVL 334
>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 = 84.3 bits (207), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 91/343 (26%), Positives = 146/343 (42%), Gaps = 73/343 (21%)
Query: 3 SCVVTVAQDGTGDYRTVQEAIDRVPLCNTRRTLIRISPGVYRQPVYVPKTKNLITLAGLC 62
+ VV+ + ++T+ +AI P +T +I I GVY + + + T+N + L G
Sbjct: 5 NAVVSKSSSDGKTFKTIADAIASAPAGSTP-FVILIKNGVYNERLTI--TRNNLHLKGES 61
Query: 63 PENTVLTWNNTATKIEHHQAARVIGTGTFGCGSVIVEGEDFVAENITFEN---------- 112
V+ A ++ + GT G ++ + +DF A+++T N
Sbjct: 62 RNGAVIAAATAAGTLKSDGSKW----GTAGSSTITISAKDFSAQSLTIRNDFDFPANQAK 117
Query: 113 ----SAPEGSGQAVAIRVT--ADRCAFYNCRFLGWQ----------YLKDCYIEGSVDFI 156
S+ QAVA+ VT DR F + +G+Q + DC I G+VDFI
Sbjct: 118 SDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFI 177
Query: 157 FGNSTALIEHCHI------HCKS---QGFITAQSRKSSQETTGYVFL--RCVITGNGGTG 205
FG+ TAL +C + KS G++TA S +Q+ G V R + +
Sbjct: 178 FGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPA 236
Query: 206 YIY-LGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNW-GKVENERS--- 246
Y LGRPW P G+ VF T MD I GW GK +N +
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 247 ----ACFYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI 285
+ F+EY+ +G G+ +K R+L D +A ++ +
Sbjct: 295 NPEDSRFFEYKSYGAGATVSKDR---RQLTDAQAAEYTQSKVL 334
>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 = 84.3 bits (207), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 91/343 (26%), Positives = 146/343 (42%), Gaps = 73/343 (21%)
Query: 3 SCVVTVAQDGTGDYRTVQEAIDRVPLCNTRRTLIRISPGVYRQPVYVPKTKNLITLAGLC 62
+ VV+ + ++T+ +AI P +T +I I GVY + + + T+N + L G
Sbjct: 5 NAVVSKSSSDGKTFKTIADAIASAPAGSTP-FVILIKNGVYNERLTI--TRNNLHLKGES 61
Query: 63 PENTVLTWNNTATKIEHHQAARVIGTGTFGCGSVIVEGEDFVAENITFEN---------- 112
V+ A ++ + GT G ++ + +DF A+++T N
Sbjct: 62 RNGAVIAAATAAGTLKSDGSKW----GTAGSSTITISAKDFSAQSLTIRNDFDFPANQAK 117
Query: 113 ----SAPEGSGQAVAIRVT--ADRCAFYNCRFLGWQ----------YLKDCYIEGSVDFI 156
S+ QAVA+ VT DR F + +G+Q + DC I G+VDFI
Sbjct: 118 SDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFI 177
Query: 157 FGNSTALIEHCHI------HCKS---QGFITAQSRKSSQETTGYVFL--RCVITGNGGTG 205
FG+ TAL +C + KS G++TA S +Q+ G V R + +
Sbjct: 178 FGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPA 236
Query: 206 YIY-LGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNW-GKVENERS--- 246
Y LGRPW P G+ VF T MD I GW GK +N +
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 247 ----ACFYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI 285
+ F+EY+ +G G+ +K R+L D +A ++ +
Sbjct: 295 NPEDSRFFEYKSYGAGATVSKDR---RQLTDAQAAEYTQSKVL 334
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 78.2 bits (191), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 84/329 (25%), Positives = 137/329 (41%), Gaps = 71/329 (21%)
Query: 3 SCVVTVAQDGTGDYRTVQEAIDRVPLCNTRRTLIRISPGVYRQPVYVPKTKNLITLAGLC 62
+ VV+ G ++ ++ A+ P +T +I + GVY + + V ++ +TL G
Sbjct: 32 NAVVSTTPQGD-EFSSINAALKSAPKDDTP-FIIFLKNGVYTERLEVARSH--VTLKGEN 87
Query: 63 PENTVLTWNNTATKIEHHQAARVIGTGTFGCGSVIVEGEDFVAENITFENS--------- 113
+ TV+ NTA + + Q + GT G +V+V +F AEN+T N
Sbjct: 88 RDGTVIG-ANTAAGMLNPQGEKW---GTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKK 143
Query: 114 -----APEGSGQAVAIRV--TADRCAFYNCRFLGWQ-----------YLKDCYIEGSVDF 155
QAVA+ + +D+ F + G+Q Y DC I G VDF
Sbjct: 144 ADTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDF 203
Query: 156 IFGNSTALIEHCHIHCKSQ-------GFITAQSRKSSQETTGYVFLRCVITGNGG--TGY 206
IFG+ + ++C+I + + G+ITA S ++ G +F+ +T G
Sbjct: 204 IFGSGITVFDNCNIVARDRSDIEPPYGYITAPSTLTTSP-YGLIFINSRLTKEPGVPANS 262
Query: 207 IYLGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNWGKVENE-------- 244
LGRPW P G+ VF T MD I GW + +
Sbjct: 263 FALGRPWHPTTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDKQGEKIWFYP 320
Query: 245 RSACFYEYRCFGPGSC--PAKRETWAREL 271
+ + F+E GPG+ +R+ A +L
Sbjct: 321 QDSRFFEANSQGPGAAINEGRRQLSAEQL 349
>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 = 46/210 (21%), Positives = 70/210 (33%), Gaps = 55/210 (26%)
Query: 16 YRTVQEAIDRVPLCNT-RRTLIRISPGVYRQPVYVPKTKNLITLAG-------------- 60
+ T+Q A+D + T +R I + PG Y+ VYVP ITL G
Sbjct: 89 HTTIQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGGITLYGTGEKPIDVKIGLSL 148
Query: 61 ------------LCPENTVLTWNNTATKIEHHQAARVIGTGTFGCGSVI-VEGEDFVAEN 107
+ P + + Q+ R G C +V + +N
Sbjct: 149 DGGMSPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVL-CSAVFWSQNNGLQLQN 207
Query: 108 ITFEN----SAPEGSGQAVAIRVTADRCAFYNCRFLGWQ--------------------- 142
+T EN S G+ AVA+R D+ N LG Q
Sbjct: 208 LTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPR 267
Query: 143 -YLKDCYIEGSVDFIFGNSTALIEHCHIHC 171
+ + YIEG VD + G + ++
Sbjct: 268 TLVTNSYIEGDVDIVSGRGAVVFDNTEFRV 297
>pdb|3VM8|A Chain A, Crystal Structure Of The Human Apobec3c Having Hiv-1
Vif-Binding Interface
pdb|3VM8|B Chain B, Crystal Structure Of The Human Apobec3c Having Hiv-1
Vif-Binding Interface
pdb|3VOW|A Chain A, Crystal Structure Of The Human Apobec3c Having Hiv-1
Vif-Binding Interface
pdb|3VOW|B Chain B, Crystal Structure Of The Human Apobec3c Having Hiv-1
Vif-Binding Interface
Length = 190
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 249 FYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI--DPDPQRPWLAQRMALRI 302
+++Y C+ G +E A E++D E ++ NF+ D +P +PW + R+
Sbjct: 125 YFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRL 180
>pdb|1LKF|A Chain A, Leukocidin F (Hlgb) From Staphylococcus Aureus
pdb|2LKF|A Chain A, Leukocidin F (Hlgb) From Staphylococcus Aureus
pdb|3LKF|A Chain A, Leukocidin F (Hlgb) From Staphylococcus Aureus With
Phosphocholine Bound
Length = 299
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 12/92 (13%)
Query: 139 LGWQYLKDCYIEGSVDFIFGNSTALIEHCHIHCKSQGFITAQSRKSSQETTGYVFLRCVI 198
LG+ + D I + +TA E I+ K + + T SR ++ + G+ I
Sbjct: 114 LGYTFGGDISISNGLSGGLNGNTAFSET--INYKQESYRTTLSRNTNYKNVGWGVEAHKI 171
Query: 199 TGNGGTGYIYLGRPWGPFGRVVFAFTYMDQCI 230
NG WGP+GR F TY ++
Sbjct: 172 MNNG----------WGPYGRDSFHPTYGNELF 193
>pdb|3B07|A Chain A, Crystal Structure Of Octameric Pore Form Of
Gamma-Hemolysin From Staphylococcus Aureus
pdb|3B07|C Chain C, Crystal Structure Of Octameric Pore Form Of
Gamma-Hemolysin From Staphylococcus Aureus
pdb|3B07|E Chain E, Crystal Structure Of Octameric Pore Form Of
Gamma-Hemolysin From Staphylococcus Aureus
pdb|3B07|G Chain G, Crystal Structure Of Octameric Pore Form Of
Gamma-Hemolysin From Staphylococcus Aureus
Length = 309
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 12/92 (13%)
Query: 139 LGWQYLKDCYIEGSVDFIFGNSTALIEHCHIHCKSQGFITAQSRKSSQETTGYVFLRCVI 198
LG+ + D I + +TA E I+ K + + T SR ++ + G+ I
Sbjct: 124 LGYTFGGDISISNGLSGGLNGNTAFSET--INYKQESYRTTLSRNTNYKNVGWGVEAHKI 181
Query: 199 TGNGGTGYIYLGRPWGPFGRVVFAFTYMDQCI 230
NG WGP+GR F TY ++
Sbjct: 182 MNNG----------WGPYGRDSFHPTYGNELF 203
>pdb|2QK7|B Chain B, A Covalent S-f Heterodimer Of Staphylococcal
Gamma-hemolysin
Length = 307
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 12/92 (13%)
Query: 139 LGWQYLKDCYIEGSVDFIFGNSTALIEHCHIHCKSQGFITAQSRKSSQETTGYVFLRCVI 198
LG+ + D I + +TA E I+ K + + T SR ++ + G+ I
Sbjct: 122 LGYTFGGDISISNGLSGGLNGNTAFSET--INYKQESYRTTLSRCTNYKNVGWGVEAHKI 179
Query: 199 TGNGGTGYIYLGRPWGPFGRVVFAFTYMDQCI 230
NG WGP+GR F TY ++
Sbjct: 180 MNNG----------WGPYGRDSFHPTYGNELF 201
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
0.324 0.138 0.455
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,112,724
Number of Sequences: 62578
Number of extensions: 450339
Number of successful extensions: 842
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 826
Number of HSP's gapped (non-prelim): 12
length of query: 306
length of database: 14,973,337
effective HSP length: 98
effective length of query: 208
effective length of database: 8,840,693
effective search space: 1838864144
effective search space used: 1838864144
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)