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= 009085
(544 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 = 295 bits (756), Expect = 3e-80, Method: Compositional matrix adjust.
Identities = 152/314 (48%), Positives = 194/314 (61%), Gaps = 13/314 (4%)
Query: 234 VTVCKDGSCKYKTLQDAVNAAPDNVPAKRFVINIKAGVYEETVRVPFEKKNVVFLGDGMG 293
V V DGS YKT+ +AV AAP++ R+VI IKAGVY E V VP +KKN++FLGDG
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPED-SKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRT 67
Query: 294 KTVITGSLNVGQQGVSTYESATVGVLGDGFMASGLTIQNTAGPDAHQAVAFRSDSDLSII 353
T+IT S NV Q G +T+ SATV +G GF+A +T QNTAG HQAVA R SDLS
Sbjct: 68 STIITASKNV-QDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAF 126
Query: 354 ENCEFLGNQDTLYAHSLRQFYKKCRIQGNVDFIFGNSPSIFQDCEILVAPRQLKPEKGEN 413
C+ L QD+LY HS RQF+ C I G VDFIFGN+ + QDC+I +P G+
Sbjct: 127 YRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDI----HARRPGSGQK 182
Query: 414 NAVTAHGRTDPAQWSGFVFQNCLINGTEEYMKLYYSKPRVHKNYLGRPWKEYSRTVFIHC 473
N VTA GRTDP Q +G V Q I T + + S P YLGRPWKEYSRTV +
Sbjct: 183 NMVTAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFP----TYLGRPWKEYSRTVVMQS 238
Query: 474 NLEALVHPDGWLPWSGDFALKTLYYGEFQNTGPGSKTANRVPWSS---QIPAEHVNAYSV 530
++ +++P GW PW G+FAL TLYYGE+QNTG G+ T+ RV W + ++
Sbjct: 239 SITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTP 298
Query: 531 QNFIQGDEWISTSS 544
+FI G W+ ++
Sbjct: 299 GSFIAGGSWLKATT 312
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 280 bits (717), Expect = 1e-75, Method: Compositional matrix adjust.
Identities = 149/321 (46%), Positives = 191/321 (59%), Gaps = 21/321 (6%)
Query: 230 LTAGVTVCKDGSCKYKTLQDAVNAAPDNVPAKRFVINIKAGVYEETVRVPFEKKNVVFLG 289
+ A V +DG+ Y+TL +AV AAPD R+VI +K G Y+E V V K N++ +G
Sbjct: 1 IIANAVVAQDGTGDYQTLAEAVAAAPDK-SKTRYVIYVKRGTYKENVEVASNKMNLMIVG 59
Query: 290 DGMGKTVITGSLNVGQQGVSTYESATVGVLGDGFMASGLTIQNTAGPDAHQAVAFRSDSD 349
DGM T ITGSLNV G +T+ SAT+ +G GF+ + IQNTAGP QAVA R +D
Sbjct: 60 DGMYATTITGSLNV-VDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGAD 118
Query: 350 LSIIENCEFLGNQDTLYAHSLRQFYKKCRIQGNVDFIFGNSPSIFQDCEILVAPRQLKPE 409
+S+I C QDTLYAHS RQFY+ + G VDFIFGN+ +FQ C+++ KP
Sbjct: 119 MSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVAR----KPG 174
Query: 410 KGENNAVTAHGRTDPAQWSGFVFQNCLINGTEEYMKLYYSKPRVHKNYLGRPWKEYSRTV 469
K + N VTA GRTDP Q +G Q C I + + + P YLGRPWKEYSRTV
Sbjct: 175 KYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFP----TYLGRPWKEYSRTV 230
Query: 470 FIHCNLEALVHPDGWLPWSGDFALKTLYYGEFQNTGPGSKTANRVPWSSQIPAEHVNA-- 527
+ L L++P GW W GDFALKTLYYGEF N GPG+ T+ RV W P HV
Sbjct: 231 VMESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKW----PGYHVITDP 286
Query: 528 -----YSVQNFIQGDEWISTS 543
++V IQG W+ ++
Sbjct: 287 AKAMPFTVAKLIQGGSWLRST 307
>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 = 2e-16, Method: Compositional matrix adjust.
Identities = 82/285 (28%), Positives = 125/285 (43%), Gaps = 57/285 (20%)
Query: 244 YKTLQDAVNAAPDNVPAKRFVINIKAGVYEETVRVPFEKKNVVFLGDGMGKTVITGS--- 300
+KT+ DA+ +AP + FVI IK GVY E R+ + N+ G+ VI +
Sbjct: 18 FKTIADAIASAP--AGSTPFVILIKNGVYNE--RLTITRNNLHLKGESRNGAVIAAATAA 73
Query: 301 --LNVGQQGVSTYESATVGVLGDGFMASGLTIQNTAGPDAHQAVAFRSDSDLSIIENCE- 357
L T S+T+ + F A LTI+N A+QA +SDSD S I++ +
Sbjct: 74 GTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQA---KSDSDSSKIKDTQA 130
Query: 358 ------------------FLGNQDTLYAHSLRQFYKKCRIQGNVDFIFGNSPSIFQDCEI 399
+G QDTLY R F+ CRI G VDFIFG+ ++F +C+
Sbjct: 131 VALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCD- 189
Query: 400 LVAPRQLKPEKGENNAVTAHGRTDPAQWSGFVFQNCLINGTEEYMKLYYSKPRVHKNY-L 458
LV+ + + G + T+ Q G V N + + S K+Y L
Sbjct: 190 LVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRV--------IRESDSVPAKSYGL 241
Query: 459 GRPWKEYS--------------RTVFIHCNLEALVHPDGWLPWSG 489
GRPW + +TVF++ +++ ++ GW SG
Sbjct: 242 GRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIY--GWDKMSG 284
>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 = 84.3 bits (207), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 82/285 (28%), Positives = 125/285 (43%), Gaps = 57/285 (20%)
Query: 244 YKTLQDAVNAAPDNVPAKRFVINIKAGVYEETVRVPFEKKNVVFLGDGMGKTVITGS--- 300
+KT+ DA+ +AP + FVI IK GVY E R+ + N+ G+ VI +
Sbjct: 18 FKTIADAIASAP--AGSTPFVILIKNGVYNE--RLTITRNNLHLKGESRNGAVIAAATAA 73
Query: 301 --LNVGQQGVSTYESATVGVLGDGFMASGLTIQNTAGPDAHQAVAFRSDSDLSIIENCE- 357
L T S+T+ + F A LTI+N A+QA +SDSD S I++ +
Sbjct: 74 GTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQA---KSDSDSSKIKDTQA 130
Query: 358 ------------------FLGNQDTLYAHSLRQFYKKCRIQGNVDFIFGNSPSIFQDCEI 399
+G QDTLY R F+ CRI G VDFIFG+ ++F +C+
Sbjct: 131 VALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCD- 189
Query: 400 LVAPRQLKPEKGENNAVTAHGRTDPAQWSGFVFQNCLINGTEEYMKLYYSKPRVHKNY-L 458
LV+ + + G + T+ Q G V N + + S K+Y L
Sbjct: 190 LVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRV--------IRESDSVPAKSYGL 241
Query: 459 GRPWKEYS--------------RTVFIHCNLEALVHPDGWLPWSG 489
GRPW + +TVF++ +++ ++ GW SG
Sbjct: 242 GRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIY--GWDKMSG 284
>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 = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 81/285 (28%), Positives = 124/285 (43%), Gaps = 57/285 (20%)
Query: 244 YKTLQDAVNAAPDNVPAKRFVINIKAGVYEETVRVPFEKKNVVFLGDGMGKTVITGS--- 300
+KT+ DA+ +AP + FVI IK GVY E R+ + N+ G+ VI +
Sbjct: 18 FKTIADAIASAP--AGSTPFVILIKNGVYNE--RLTITRNNLHLKGESRNGAVIAAATAA 73
Query: 301 --LNVGQQGVSTYESATVGVLGDGFMASGLTIQNTAGPDAHQAVAFRSDSDLSIIENCE- 357
L T S+T+ + F A LTI+N A+QA +SDSD S I++ +
Sbjct: 74 GTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQA---KSDSDSSKIKDTQA 130
Query: 358 ------------------FLGNQDTLYAHSLRQFYKKCRIQGNVDFIFGNSPSIFQDCEI 399
+G Q TLY R F+ CRI G VDFIFG+ ++F +C+
Sbjct: 131 VALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCD- 189
Query: 400 LVAPRQLKPEKGENNAVTAHGRTDPAQWSGFVFQNCLINGTEEYMKLYYSKPRVHKNY-L 458
LV+ + + G + T+ Q G V N + + S K+Y L
Sbjct: 190 LVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRV--------IRESDSVPAKSYGL 241
Query: 459 GRPWKEYS--------------RTVFIHCNLEALVHPDGWLPWSG 489
GRPW + +TVF++ +++ ++ GW SG
Sbjct: 242 GRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIY--GWDKMSG 284
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 90/336 (26%), Positives = 146/336 (43%), Gaps = 72/336 (21%)
Query: 243 KYKTLQDAVNAAP-DNVPAKRFVINIKAGVYEETVRVPFEKKNVVFLGDGMGKTVI---- 297
++ ++ A+ +AP D+ P F+I +K GVY E R+ + +V G+ TVI
Sbjct: 43 EFSSINAALKSAPKDDTP---FIIFLKNGVYTE--RLEVARSHVTLKGENRDGTVIGANT 97
Query: 298 -TGSLNVGQQGVSTYESATVGVLGDGFMASGLTIQNTAGPDAH--------------QAV 342
G LN + T S+TV V F A LTI+N A+ QAV
Sbjct: 98 AAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAV 157
Query: 343 AF--RSDSDLSIIENCEFLGNQDTLYAHS-LRQFYKKCRIQGNVDFIFGNSPSIFQDCEI 399
A +SD + + + G QDTLY+ + R ++ C I G+VDFIFG+ ++F +C I
Sbjct: 158 ALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCNI 217
Query: 400 LVAPR-QLKPEKGENNAVTAHGRTDPAQWSGFVFQNCLINGTEEYMKLYYSKPRVHKN-- 456
+ R ++P G +TA + + G +F N + +P V N
Sbjct: 218 VARDRSDIEPPYG---YITAPSTLTTSPY-GLIFINSRLT----------KEPGVPANSF 263
Query: 457 YLGRPWKEYS--------------RTVFIHCNLEALVHPDGWLPWSGD--------FALK 494
LGRPW + ++VFI+ ++ ++ GW SG F +
Sbjct: 264 ALGRPWHPTTTFADGRYADPAAIGQSVFINTTMDDHIY--GWDKMSGKDKQGEKIWFYPQ 321
Query: 495 TLYYGEFQNTGPGSKTANRVPWSSQIPAEHVNAYSV 530
+ E + GPG+ Q+ AE + A+++
Sbjct: 322 DSRFFEANSQGPGAAINEG---RRQLSAEQLKAFTL 354
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 54/219 (24%), Positives = 79/219 (36%), Gaps = 51/219 (23%)
Query: 242 CKYKTLQDAVNAAPDNVPAKRFVINIKAGVYEETVRVPFEKKNVVFLGDGMGKTVITGSL 301
+ T+Q AV+AA KR I + G Y+ TV VP + G G + L
Sbjct: 87 VTHTTIQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGGITLYGTGEKPIDVKIGL 146
Query: 302 NV---------------------GQQGVSTYESA------TVGVL--------GDGFMAS 326
++ G+ Y+S ++GVL +G
Sbjct: 147 SLDGGMSPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLCSAVFWSQNNGLQLQ 206
Query: 327 GLTIQNTAGPDA----HQAVAFRSDSDLSIIENCEFLGNQDTLYA------------HSL 370
LTI+NT G H AVA R+D D I N LG Q+T +
Sbjct: 207 NLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQP 266
Query: 371 RQFYKKCRIQGNVDFIFGNSPSIFQDCEILVAPRQLKPE 409
R I+G+VD + G +F + E V + + E
Sbjct: 267 RTLVTNSYIEGDVDIVSGRGAVVFDNTEFRVVNSRTQQE 305
>pdb|4DTD|A Chain A, Structure And Functional Characterization Of A Vibrio
Cholerae Toxin From The MartxVGRG FAMILY
Length = 396
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/109 (22%), Positives = 46/109 (42%)
Query: 67 NPSPAQMIQSAIGVSSQNLETAKSMVKRILDSSSDSQNRSRAATTCLQILGYSGARSQSA 126
N P IQS G + AK ++ S++SQ ++ T Q A
Sbjct: 126 NHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITXTPSGQQATVGVAAKGFG 185
Query: 127 SDALPRGKLKDARAWYSAALTYQYDCWSALKYVNDTKQVGETMAFLDSL 175
+ A P +L ++ WY +L Q+ ++ + ++D + A+L S+
Sbjct: 186 TSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSI 234
>pdb|4DTL|A Chain A, Structure Of A Vgrg Vibrio Cholerae Toxin Acd Domain In
Complex With Atp And Mn++
Length = 396
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 32/140 (22%), Positives = 56/140 (40%), Gaps = 7/140 (5%)
Query: 67 NPSPAQMIQSAIGVSSQNLETAKSMVKRILDSSSDSQNRSRAATTCLQILGYSGARSQSA 126
N P IQS G + AK ++ S++SQ ++ T Q A
Sbjct: 126 NHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITMTPSGQQATVGVAAKGFG 185
Query: 127 SDALPRGKLKDARAWYSAALTYQYDCWSALKYVNDTKQVGETMAFLDSLTGLTSNALSMM 186
+ A P +L ++ WY +L Q+ ++ + ++D + A+L S+ T+
Sbjct: 186 TSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAK-- 243
Query: 187 MSFDNFGDDFNAWRAPQTER 206
FG N W P +E+
Sbjct: 244 ----KFGIYINEWD-PMSEQ 258
>pdb|4E1F|A Chain A, Structure Of A Vgrg Vibrio Cholerae Toxin Acd Domain
Glu16gln Mutant In Complex With Adp And Mn++
Length = 396
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 32/140 (22%), Positives = 56/140 (40%), Gaps = 7/140 (5%)
Query: 67 NPSPAQMIQSAIGVSSQNLETAKSMVKRILDSSSDSQNRSRAATTCLQILGYSGARSQSA 126
N P IQS G + AK ++ S++SQ ++ T Q A
Sbjct: 126 NHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITMTPSGQQATVGVAAKGFG 185
Query: 127 SDALPRGKLKDARAWYSAALTYQYDCWSALKYVNDTKQVGETMAFLDSLTGLTSNALSMM 186
+ A P +L ++ WY +L Q+ ++ + ++D + A+L S+ T+
Sbjct: 186 TSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAK-- 243
Query: 187 MSFDNFGDDFNAWRAPQTER 206
FG N W P +E+
Sbjct: 244 ----KFGIYINEWD-PMSEQ 258
>pdb|4DTF|A Chain A, Structure Of A Vgrg Vibrio Cholerae Toxin Acd Domain In
Complex With Amp-Pnp And Mg++
pdb|4DTH|A Chain A, Structure Of A Vgrg Vibrio Cholerae Toxin Acd Domain In
Complex With Atp And Mg++
pdb|4E1C|A Chain A, Structure Of A Vgrg Vibrio Cholerae Toxin Acd Domain In
Complex With Adp And Mg++
pdb|4E1D|A Chain A, Structure Of A Vgrg Vibrio Cholerae Toxin Acd Domain In
Complex With Adp And Mn++
Length = 396
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 32/140 (22%), Positives = 56/140 (40%), Gaps = 7/140 (5%)
Query: 67 NPSPAQMIQSAIGVSSQNLETAKSMVKRILDSSSDSQNRSRAATTCLQILGYSGARSQSA 126
N P IQS G + AK ++ S++SQ ++ T Q A
Sbjct: 126 NHQPLAPIQSEDGRFVIEITNAKHVIAAGNGISAESQGQTITMTPSGQQATVGVAAKGFG 185
Query: 127 SDALPRGKLKDARAWYSAALTYQYDCWSALKYVNDTKQVGETMAFLDSLTGLTSNALSMM 186
+ A P +L ++ WY +L Q+ ++ + ++D + A+L S+ T+
Sbjct: 186 TSATPELRLLESAPWYQKSLKSQFASLTSAENLDDKELAANVFAYLTSIYLKTAELAK-- 243
Query: 187 MSFDNFGDDFNAWRAPQTER 206
FG N W P +E+
Sbjct: 244 ----KFGIYINEWD-PMSEQ 258
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
0.317 0.131 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,889,488
Number of Sequences: 62578
Number of extensions: 681981
Number of successful extensions: 1563
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1536
Number of HSP's gapped (non-prelim): 17
length of query: 544
length of database: 14,973,337
effective HSP length: 104
effective length of query: 440
effective length of database: 8,465,225
effective search space: 3724699000
effective search space used: 3724699000
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)