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= 021162
(316 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 = 180 bits (457), Expect = 8e-46, Method: Compositional matrix adjust.
Identities = 108/307 (35%), Positives = 154/307 (50%), Gaps = 30/307 (9%)
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 VTADRCAFYNCRFLGWQDTLYLHYGKQYLKDCYIEGSVDFIFGNSTALIEHCHIHCKSQG 185
V +D AFY C L +QD+LY+H +Q+ +C+I G+VDFIFGN+ +++ C IH + G
Sbjct: 119 VGSDLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPG 178
Query: 186 -----FITAQSRKSSQETTGYVFLRCVITGNGGTGYI---------YLGRPWGPFGRVVF 231
+TAQ R + TG V + I G T + YLGRPW + R V
Sbjct: 179 SGQKNMVTAQGRTDPNQNTGIVIQKSRI---GATSDLQPVQSSFPTYLGRPWKEYSRTVV 235
Query: 232 AFTYMDQCIRHVGWHNWGKVENERSACFYEYRCFGPGSCPAKRETWARELL---DEEAEQ 288
+ + I GW W + + EY+ G G+ + R TW + EA+
Sbjct: 236 MQSSITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQG 295
Query: 289 FLMHNFI 295
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 = 152 bits (384), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 89/281 (31%), Positives = 135/281 (48%), Gaps = 21/281 (7%)
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 ADRCAFYNCRFLGWQDTLYLHYGKQYLKDCYIEGSVDFIFGNSTALIEHCHIHCKS---- 183
AD CR +QDTLY H +Q+ +D Y+ G+VDFIFGN+ + + C + +
Sbjct: 117 ADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKY 176
Query: 184 -QGFITAQSRKSSQETTGYVFLRCVITGNGGTGYI------YLGRPWGPFGRVVFAFTYM 236
Q +TAQ R + TG C I + + YLGRPW + R V +Y+
Sbjct: 177 QQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYL 236
Query: 237 DQCIRHVGWHNWGKVENERSACFYEYRCFGPGSCPAKRETW 277
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 = 103 bits (256), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 96/343 (27%), Positives = 153/343 (44%), Gaps = 63/343 (18%)
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--ADRCAFYNCRFLGWQDTLYLHYGKQYLKDCYIEGSVDFI 166
S+ QAVA+ VT DR F + +G+QDTLY+ G+ + DC I G+VDFI
Sbjct: 118 SDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFI 177
Query: 167 FGNSTALIEHCHI------HCKS---QGFITAQSRKSSQETTGYVFL--RCVITGNGGTG 215
FG+ TAL +C + KS G++TA S +Q+ G V R + +
Sbjct: 178 FGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPA 236
Query: 216 YIY-LGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNW-GKVENERS--- 256
Y LGRPW P G+ VF T MD I GW GK +N +
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 257 ----ACFYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI 295
+ F+EY+ +G G+ +K R+L D +A ++ +
Sbjct: 295 NPEDSRFFEYKSYGAGAAVSKDR---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 = 102 bits (255), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 96/343 (27%), Positives = 153/343 (44%), Gaps = 63/343 (18%)
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--ADRCAFYNCRFLGWQDTLYLHYGKQYLKDCYIEGSVDFI 166
S+ QAVA+ VT DR F + +G+QDTLY+ G+ + DC I G+VDFI
Sbjct: 118 SDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFI 177
Query: 167 FGNSTALIEHCHI------HCKS---QGFITAQSRKSSQETTGYVFL--RCVITGNGGTG 215
FG+ TAL +C + KS G++TA S +Q+ G V R + +
Sbjct: 178 FGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPA 236
Query: 216 YIY-LGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNW-GKVENERS--- 256
Y LGRPW P G+ VF T MD I GW GK +N +
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 257 ----ACFYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI 295
+ F+EY+ +G G+ +K R+L D +A ++ +
Sbjct: 295 NPEDSRFFEYKSYGAGATVSKDR---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 = 99.4 bits (246), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 95/343 (27%), Positives = 152/343 (44%), Gaps = 63/343 (18%)
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--ADRCAFYNCRFLGWQDTLYLHYGKQYLKDCYIEGSVDFI 166
S+ QAVA+ VT DR F + +G+Q TLY+ G+ + DC I G+VDFI
Sbjct: 118 SDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFI 177
Query: 167 FGNSTALIEHCHI------HCKS---QGFITAQSRKSSQETTGYVFL--RCVITGNGGTG 215
FG+ TAL +C + KS G++TA S +Q+ G V R + +
Sbjct: 178 FGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQK-YGLVITNSRVIRESDSVPA 236
Query: 216 YIY-LGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNW-GKVENERS--- 256
Y LGRPW P G+ VF T MD I GW GK +N +
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 257 ----ACFYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI 295
+ 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 = 92.0 bits (227), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 89/329 (27%), Positives = 143/329 (43%), Gaps = 61/329 (18%)
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--TADRCAFYNCRFLGWQDTLYLHYG-KQYLKDCYIEGSVDF 165
QAVA+ + +D+ F + G+QDTLY G + Y DC I G VDF
Sbjct: 144 ADTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDF 203
Query: 166 IFGNSTALIEHCHIHCKSQ-------GFITAQSRKSSQETTGYVFLRCVITGNGG--TGY 216
IFG+ + ++C+I + + G+ITA S ++ G +F+ +T G
Sbjct: 204 IFGSGITVFDNCNIVARDRSDIEPPYGYITAPSTLTTSP-YGLIFINSRLTKEPGVPANS 262
Query: 217 IYLGRPWGP--------------FGRVVFAFTYMDQCIRHVGWHNWGKVENE-------- 254
LGRPW P G+ VF T MD I GW + +
Sbjct: 263 FALGRPWHPTTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDKQGEKIWFYP 320
Query: 255 RSACFYEYRCFGPGSC--PAKRETWAREL 281
+ + F+E GPG+ +R+ A +L
Sbjct: 321 QDSRFFEANSQGPGAAINEGRRQLSAEQL 349
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 49/210 (23%), Positives = 76/210 (36%), Gaps = 45/210 (21%)
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----SAPEGSGQAVAIRVTADRCAFYNCRFLGWQDTLY---------LHYGKQ-- 152
+T EN S G+ AVA+R D+ N LG Q+T + L +Q
Sbjct: 208 LTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPR 267
Query: 153 -YLKDCYIEGSVDFIFGNSTALIEHCHIHC 181
+ + 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 = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 259 FYEYRCFGPGSCPAKRETWARELLDEEAEQFLMHNFI--DPDPQRPWLAQRMALRI 312
+++Y C+ G +E A E++D E ++ NF+ D +P +PW + R+
Sbjct: 125 YFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRL 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
0.324 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: 10,508,586
Number of Sequences: 62578
Number of extensions: 471358
Number of successful extensions: 878
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 861
Number of HSP's gapped (non-prelim): 12
length of query: 316
length of database: 14,973,337
effective HSP length: 99
effective length of query: 217
effective length of database: 8,778,115
effective search space: 1904850955
effective search space used: 1904850955
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)