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= 046674
(261 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 = 175 bits (443), Expect = 3e-44, Method: Compositional matrix adjust.
Identities = 101/271 (37%), Positives = 143/271 (52%), Gaps = 17/271 (6%)
Query: 7 IRVDQSGRGDFKKIQDAIDSVPSNNSKLYFIWIKPGTYREKIVVPADKPFITISGTKASN 66
+ V G GD+K + +A+ + P ++ Y I IK G YRE + VP K I G ++
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTS 68
Query: 67 TIITWS----DGGEIFQSATFTVMASDFVGRFLTIENTYGSAG-KAVALRVSANRAAFYG 121
TIIT S DG F SAT + + F+ R +T +NT G+A +AVALRV ++ +AFY
Sbjct: 69 TIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYR 128
Query: 122 CRILSYQDTLLDDTGNHYYSSCYIEGATDFICGNAASLFERCHIHSLSTGNGA---ITAQ 178
C IL+YQD+L + ++ +C+I G DFI GNAA + + C IH+ G+G +TAQ
Sbjct: 129 CDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQ 188
Query: 179 KRVSSEENTGFTFLGCKITGVG---------KAVLGRPWGPYSRVVYALTYMSGLVLPQG 229
R +NTG +I LGRPW YSR V + ++ ++ P G
Sbjct: 189 GRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAG 248
Query: 230 WNDWHDYAKHTNVYYGEYKCYGPGADRSSRV 260
W W +YYGEY+ G GA S RV
Sbjct: 249 WFPWDGNFALDTLYYGEYQNTGAGAATSGRV 279
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 167 bits (422), Expect = 6e-42, Method: Compositional matrix adjust.
Identities = 100/270 (37%), Positives = 142/270 (52%), Gaps = 19/270 (7%)
Query: 9 VDQSGRGDFKKIQDAIDSVPSNNSKLYFIWIKPGTYREKIVVPADKPFITISGTKASNTI 68
V Q G GD++ + +A+ + P + Y I++K GTY+E + V ++K + I G T
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATT 66
Query: 69 ITWS----DGGEIFQSATFTVMASDFVGRFLTIENTYGSA-GKAVALRVSANRAAFYGCR 123
IT S DG F+SAT + F+ + + I+NT G A +AVALRV A+ + CR
Sbjct: 67 ITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCR 126
Query: 124 ILSYQDTLLDDTGNHYYSSCYIEGATDFICGNAASLFERCHIHSLSTG---NGAITAQKR 180
I +YQDTL + +Y Y+ G DFI GNAA +F++C + + G +TAQ R
Sbjct: 127 IDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGR 186
Query: 181 VSSEENTGFTFLGCKITGVGK---------AVLGRPWGPYSRVVYALTYMSGLVLPQGWN 231
+ TG + C I LGRPW YSR V +Y+ GL+ P GW
Sbjct: 187 TDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWA 246
Query: 232 DWH-DYAKHTNVYYGEYKCYGPGADRSSRV 260
+W D+A T +YYGE+ GPGA S RV
Sbjct: 247 EWDGDFALKT-LYYGEFMNNGPGAGTSKRV 275
>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 = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 83/298 (27%), Positives = 120/298 (40%), Gaps = 64/298 (21%)
Query: 17 FKKIQDAIDSVPSNNSKLYFIWIKPGTYREKIVVPADKPFI------TISGTKASNTIIT 70
FK I DAI S P+ S + I IK G Y E++ + + + A+
Sbjct: 18 FKTIADAIASAPAG-STPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 71 WSDGGE--IFQSATFTVMASDFVGRFLTIENTYGSAG---------------KAVALRV- 112
SDG + S+T T+ A DF + LTI N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 113 -SANRAAFYGCRILSYQDTLLDDTGNHYYSSCYIEGATDFICGNAASLFERCHIHS---- 167
S +RA F ++ YQDTL G ++S C I G DFI G+ +LF C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 168 -LSTGN--GAITAQKRVSSEENTGFTFLGCKITGVGKAV------LGRPWGPYS------ 212
+ +GN G +TA + + G ++ +V LGRPW P +
Sbjct: 197 DVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 213 --------RVVYALTYMSGLVLPQGWNDWHDYAKHTNVY--------YGEYKCYGPGA 254
+ V+ T M + GW+ K+ N + EYK YG GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGA 311
>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 = 76.3 bits (186), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 83/298 (27%), Positives = 120/298 (40%), Gaps = 64/298 (21%)
Query: 17 FKKIQDAIDSVPSNNSKLYFIWIKPGTYREKIVVPADKPFI------TISGTKASNTIIT 70
FK I DAI S P+ S + I IK G Y E++ + + + A+
Sbjct: 18 FKTIADAIASAPAG-STPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 71 WSDGGE--IFQSATFTVMASDFVGRFLTIENTYGSAG---------------KAVALRV- 112
SDG + S+T T+ A DF + LTI N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 113 -SANRAAFYGCRILSYQDTLLDDTGNHYYSSCYIEGATDFICGNAASLFERCHIHS---- 167
S +RA F ++ YQDTL G ++S C I G DFI G+ +LF C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 168 -LSTGN--GAITAQKRVSSEENTGFTFLGCKITGVGKAV------LGRPWGPYS------ 212
+ +GN G +TA + + G ++ +V LGRPW P +
Sbjct: 197 DVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 213 --------RVVYALTYMSGLVLPQGWNDWHDYAKHTNVY--------YGEYKCYGPGA 254
+ V+ T M + GW+ K+ N + EYK YG GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGA 311
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 75.5 bits (184), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 68/241 (28%), Positives = 108/241 (44%), Gaps = 43/241 (17%)
Query: 9 VDQSGRGD-FKKIQDAIDSVPSNNSKLYFIWIKPGTYREKIVVPADKPFITISGTKASNT 67
V + +GD F I A+ S P +++ + I++K G Y E++ V + +T+ G T
Sbjct: 35 VSTTPQGDEFSSINAALKSAPKDDTP-FIIFLKNGVYTERLEVA--RSHVTLKGENRDGT 91
Query: 68 IITWSDGGEIFQ----------SATFTVMASDFVGRFLTIENTYGSAG------------ 105
+I + + S+T V A +F LTI N +
Sbjct: 92 VIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKL 151
Query: 106 ---KAVALRVSAN--RAAFYGCRILSYQDTLLDDTGNH-YYSSCYIEGATDFICGNAASL 159
+AVAL ++ N +A F ++ YQDTL TG+ Y+S C I G DFI G+ ++
Sbjct: 152 KDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITV 211
Query: 160 FERCHI-----HSLSTGNGAITAQKRVSSEENTGFTFLGCKIT---GV--GKAVLGRPWG 209
F+ C+I + G ITA +++ G F+ ++T GV LGRPW
Sbjct: 212 FDNCNIVARDRSDIEPPYGYITAPSTLTTSP-YGLIFINSRLTKEPGVPANSFALGRPWH 270
Query: 210 P 210
P
Sbjct: 271 P 271
>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 = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 82/298 (27%), Positives = 119/298 (39%), Gaps = 64/298 (21%)
Query: 17 FKKIQDAIDSVPSNNSKLYFIWIKPGTYREKIVVPADKPFI------TISGTKASNTIIT 70
FK I DAI S P+ S + I IK G Y E++ + + + A+
Sbjct: 18 FKTIADAIASAPAG-STPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 71 WSDGGE--IFQSATFTVMASDFVGRFLTIENTYGSAG---------------KAVALRV- 112
SDG + S+T T+ A DF + LTI N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 113 -SANRAAFYGCRILSYQDTLLDDTGNHYYSSCYIEGATDFICGNAASLFERCHIHS---- 167
S +RA F ++ YQ TL G ++S C I G DFI G+ +LF C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 168 -LSTGN--GAITAQKRVSSEENTGFTFLGCKITGVGKAV------LGRPWGPYS------ 212
+ +GN G +TA + + G ++ +V LGRPW P +
Sbjct: 197 DVKSGNVSGYLTAPS-TNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGR 255
Query: 213 --------RVVYALTYMSGLVLPQGWNDWHDYAKHTNVY--------YGEYKCYGPGA 254
+ V+ T M + GW+ K+ N + EYK YG GA
Sbjct: 256 YADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGA 311
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 51/209 (24%), Positives = 76/209 (36%), Gaps = 58/209 (27%)
Query: 20 IQDAIDS-VPSNNSKLYFIWIKPGTYREKIVVPADKPFITISGT--KASNTIITWS-DGG 75
IQ A+D+ + +K +I + PG Y+ + VPA IT+ GT K + I S DGG
Sbjct: 92 IQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGGITLYGTGEKPIDVKIGLSLDGG 151
Query: 76 E-------------------------------------IFQSATFTVMASDFVGRFLTIE 98
+ SA F + + LTIE
Sbjct: 152 MSPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLCSAVFWSQNNGLQLQNLTIE 211
Query: 99 NTYG---SAGK--AVALRVSANRAAFYGCRILSYQDTLL------------DDTGNHYYS 141
NT G AG AVALR ++ IL Q+T + +
Sbjct: 212 NTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPRTLVT 271
Query: 142 SCYIEGATDFICGNAASLFERCHIHSLST 170
+ YIEG D + G A +F+ +++
Sbjct: 272 NSYIEGDVDIVSGRGAVVFDNTEFRVVNS 300
>pdb|1PVL|A Chain A, Structure Of The Panton-Valentine Leucocidin F Component
From Staphylococcus Aureus
Length = 301
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 180 RVSSEENTGFTFLGCKITGVGKAVLGRPWGPYSRVVYALTYMSGLVL 226
R S ++ T F +G + ++ WGPY R Y TY + + L
Sbjct: 150 RTSLDKRTNFKKIGWDVEA--HKIMNNGWGPYGRDSYHSTYGNEMFL 194
>pdb|1Q57|A Chain A, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|B Chain B, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|C Chain C, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|D Chain D, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|E Chain E, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|F Chain F, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|G Chain G, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
Length = 503
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 178 QKRVSSEENTGFTFLGCKITGVGKAVLGRPWGPYSRVVYALTYMSGLVL 226
++ +SSEE+ G F GC TG+ LG G V +T SG+V+
Sbjct: 213 REHLSSEESVGLLFSGC--TGINDKTLGARGGE----VIMVTSGSGMVM 255
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
0.320 0.135 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,503,500
Number of Sequences: 62578
Number of extensions: 360819
Number of successful extensions: 835
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: 818
Number of HSP's gapped (non-prelim): 12
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
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: 50 (23.9 bits)