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= 036696
(528 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 = 341 bits (875), Expect = 5e-94, Method: Compositional matrix adjust.
Identities = 169/315 (53%), Positives = 208/315 (66%), Gaps = 3/315 (0%)
Query: 214 NLVVATDGSGNYRTIQAAINAAAGRRGSGRFIIHVKRGVYRENIEVGLNNNNIMLVGEGM 273
N+VVA DGSG+Y+T+ A+ AAA R++I +K GVYREN++V NIM +G+G
Sbjct: 8 NVVVAADGSGDYKTVSEAV-AAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGR 66
Query: 274 RNTIIXXXXXXXXXXXXXXXXXXXIDGLHFMGRDITFQNTAGPLKGQAVALRSASDLSVF 333
+TII G F+ RDITFQNTAG K QAVALR SDLS F
Sbjct: 67 TSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAF 126
Query: 334 YRCAFQGYQDTLMVHSQRQFYKKCYIYGTIDFIFGNAAVVFQNCIIFVRKPLKGQANVIT 393
YRC YQD+L VHS RQF+ C+I GT+DFIFGNAAVV Q+C I R+P GQ N++T
Sbjct: 127 YRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVT 186
Query: 394 AQGRNDPFQNTAISIHSSRVLPANDLKPVVRNFKTYLGRPWQQYSRTVILKTYIDGFVSP 453
AQGR DP QNT I I SR+ +DL+PV +F TYLGRPW++YSRTV++++ I ++P
Sbjct: 187 AQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINP 246
Query: 454 LGWSTWSPGNNFALDTLFYGEYENYGPGSSTRHRVKWRGFHVITSPKVASQFTVGSLIAG 513
GW W NFALDTL+YGEY+N G G++T RV W+GF VITS A FT GS IAG
Sbjct: 247 AGWFPWD--GNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAG 304
Query: 514 RSWLPATGVPFILGL 528
SWL AT PF LGL
Sbjct: 305 GSWLKATTFPFSLGL 319
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 336 bits (862), Expect = 2e-92, Method: Compositional matrix adjust.
Identities = 162/316 (51%), Positives = 211/316 (66%), Gaps = 3/316 (0%)
Query: 213 ANLVVATDGSGNYRTIQAAINAAAGRRGSGRFIIHVKRGVYRENIEVGLNNNNIMLVGEG 272
AN VVA DG+G+Y+T+ A+ AAA + R++I+VKRG Y+EN+EV N N+M+VG+G
Sbjct: 3 ANAVVAQDGTGDYQTLAEAV-AAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDG 61
Query: 273 MRNTIIXXXXXXXXXXXXXXXXXXXIDGLHFMGRDITFQNTAGPLKGQAVALRSASDLSV 332
M T I G F+ +DI QNTAGP K QAVALR +D+SV
Sbjct: 62 MYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSV 121
Query: 333 FYRCAFQGYQDTLMVHSQRQFYKKCYIYGTIDFIFGNAAVVFQNCIIFVRKPLKGQANVI 392
RC YQDTL HSQRQFY+ Y+ GT+DFIFGNAAVVFQ C + RKP K Q N++
Sbjct: 122 INRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMV 181
Query: 393 TAQGRNDPFQNTAISIHSSRVLPANDLKPVVRNFKTYLGRPWQQYSRTVILKTYIDGFVS 452
TAQGR DP Q T SI ++ ++DL+PV++ F TYLGRPW++YSRTV++++Y+ G ++
Sbjct: 182 TAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLIN 241
Query: 453 PLGWSTWSPGNNFALDTLFYGEYENYGPGSSTRHRVKWRGFHVITSPKVASQFTVGSLIA 512
P GW+ W +FAL TL+YGE+ N GPG+ T RVKW G+HVIT P A FTV LI
Sbjct: 242 PAGWAEWD--GDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQ 299
Query: 513 GRSWLPATGVPFILGL 528
G SWL +TGV ++ GL
Sbjct: 300 GGSWLRSTGVAYVDGL 315
>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 = 82.0 bits (201), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 93/315 (29%), Positives = 134/315 (42%), Gaps = 63/315 (20%)
Query: 218 ATDGSGNYRTIQAAINAAAGRRGSGRFIIHVKRGVYRENIEVGLNNNNIMLVGEGMRNTI 277
++DG ++TI AI +A GS F+I +K GVY E + + NN+ L GE RN
Sbjct: 12 SSDGK-TFKTIADAIASAPA--GSTPFVILIKNGVYNERLTI--TRNNLHLKGES-RNGA 65
Query: 278 IXXXXXXXXXXXX-------XXXXXXXIDGLHFMGRDITFQNT-------------AGPL 317
+ I F + +T +N + +
Sbjct: 66 VIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKI 125
Query: 318 KG-QAVAL--RSASDLSVFYRCAFQGYQDTLMVHSQRQFYKKCYIYGTIDFIFGNAAVVF 374
K QAVAL + D + F + GYQDTL V R F+ C I GT+DFIFG+ +F
Sbjct: 126 KDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
Query: 375 QNCIIFVR-KPLKGQANV---ITAQGRNDPFQNTAISIHSSRVLPANDLKPVVRNFKTY- 429
NC + R + NV +TA N Q + I +SRV+ +D P K+Y
Sbjct: 186 NNCDLVSRYRADVKSGNVSGYLTAPSTN-INQKYGLVITNSRVIRESDSVPA----KSYG 240
Query: 430 LGRPWQQYS--------------RTVILKTYIDGFVSPLGWSTWSP----GNNFAL---D 468
LGRPW + +TV L T +D + GW S GN D
Sbjct: 241 LGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPED 298
Query: 469 TLFYGEYENYGPGSS 483
+ F+ EY++YG G++
Sbjct: 299 SRFF-EYKSYGAGAT 312
>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 = 82.0 bits (201), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 93/315 (29%), Positives = 134/315 (42%), Gaps = 63/315 (20%)
Query: 218 ATDGSGNYRTIQAAINAAAGRRGSGRFIIHVKRGVYRENIEVGLNNNNIMLVGEGMRNTI 277
++DG ++TI AI +A GS F+I +K GVY E + + NN+ L GE RN
Sbjct: 12 SSDGK-TFKTIADAIASAPA--GSTPFVILIKNGVYNERLTI--TRNNLHLKGES-RNGA 65
Query: 278 IXXXXXXXXXXXX-------XXXXXXXIDGLHFMGRDITFQNT-------------AGPL 317
+ I F + +T +N + +
Sbjct: 66 VIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKI 125
Query: 318 KG-QAVAL--RSASDLSVFYRCAFQGYQDTLMVHSQRQFYKKCYIYGTIDFIFGNAAVVF 374
K QAVAL + D + F + GYQDTL V R F+ C I GT+DFIFG+ +F
Sbjct: 126 KDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
Query: 375 QNCIIFVR-KPLKGQANV---ITAQGRNDPFQNTAISIHSSRVLPANDLKPVVRNFKTY- 429
NC + R + NV +TA N Q + I +SRV+ +D P K+Y
Sbjct: 186 NNCDLVSRYRADVKSGNVSGYLTAPSTN-INQKYGLVITNSRVIRESDSVPA----KSYG 240
Query: 430 LGRPWQQYS--------------RTVILKTYIDGFVSPLGWSTWSP----GNNFAL---D 468
LGRPW + +TV L T +D + GW S GN D
Sbjct: 241 LGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPED 298
Query: 469 TLFYGEYENYGPGSS 483
+ F+ EY++YG G++
Sbjct: 299 SRFF-EYKSYGAGAA 312
>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 = 78.6 bits (192), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 92/315 (29%), Positives = 133/315 (42%), Gaps = 63/315 (20%)
Query: 218 ATDGSGNYRTIQAAINAAAGRRGSGRFIIHVKRGVYRENIEVGLNNNNIMLVGEGMRNTI 277
++DG ++TI AI +A GS F+I +K GVY E + + NN+ L GE RN
Sbjct: 12 SSDGK-TFKTIADAIASAPA--GSTPFVILIKNGVYNERLTI--TRNNLHLKGES-RNGA 65
Query: 278 IXXXXXXXXXXXX-------XXXXXXXIDGLHFMGRDITFQNT-------------AGPL 317
+ I F + +T +N + +
Sbjct: 66 VIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKI 125
Query: 318 KG-QAVAL--RSASDLSVFYRCAFQGYQDTLMVHSQRQFYKKCYIYGTIDFIFGNAAVVF 374
K QAVAL + D + F + GYQ TL V R F+ C I GT+DFIFG+ +F
Sbjct: 126 KDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALF 185
Query: 375 QNCIIFVR-KPLKGQANV---ITAQGRNDPFQNTAISIHSSRVLPANDLKPVVRNFKTY- 429
NC + R + NV +TA N Q + I +SRV+ +D P K+Y
Sbjct: 186 NNCDLVSRYRADVKSGNVSGYLTAPSTN-INQKYGLVITNSRVIRESDSVPA----KSYG 240
Query: 430 LGRPWQQYS--------------RTVILKTYIDGFVSPLGWSTWSP----GNNFAL---D 468
LGRPW + +TV L T +D + GW S GN D
Sbjct: 241 LGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWFNPED 298
Query: 469 TLFYGEYENYGPGSS 483
+ F+ EY++YG G++
Sbjct: 299 SRFF-EYKSYGAGAT 312
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 71.6 bits (174), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 89/353 (25%), Positives = 140/353 (39%), Gaps = 74/353 (20%)
Query: 211 ARANLVVATDGSGN-YRTIQAAINAAAGRRGSGRFIIHVKRGVYRENIEVGLNNNNIMLV 269
A+ N VV+T G+ + +I AA+ +A + FII +K GVY E +EV +++ L
Sbjct: 29 AQYNAVVSTTPQGDEFSSINAALKSAP--KDDTPFIIFLKNGVYTERLEVA--RSHVTLK 84
Query: 270 GEGMRNTIIXXXXXXXXXXX------XXXXXXXXIDGLHFMGRDITFQNT---------- 313
GE T+I ++ +F ++T +N
Sbjct: 85 GENRDGTVIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKA 144
Query: 314 -AGPLK---GQAVALRSA--SDLSVFYRCAFQGYQDTLMVHS-QRQFYKKCYIYGTIDFI 366
P K QAVAL A SD + F +GYQDTL + R ++ C I G +DFI
Sbjct: 145 DTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFI 204
Query: 367 FGNAAVVFQNCIIFVR-----KPLKG---QANVITAQGRNDPFQNTAISIHSSRVLPAND 418
FG+ VF NC I R +P G + +T F N+ ++ +PAN
Sbjct: 205 FGSGITVFDNCNIVARDRSDIEPPYGYITAPSTLTTSPYGLIFINSRLTKEPG--VPANS 262
Query: 419 LKPVVRNFKTYLGRPWQQYS--------------RTVILKTYIDGFVSPLGWSTWSPGNN 464
LGRPW + ++V + T +D + GW S +
Sbjct: 263 FA---------LGRPWHPTTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDK 311
Query: 465 -------FALDTLFYGEYENYGPGSST---RHRVKWRGFHVITSPKVASQFTV 507
+ D+ F+ E + GPG++ R ++ T P + + V
Sbjct: 312 QGEKIWFYPQDSRFF-EANSQGPGAAINEGRRQLSAEQLKAFTLPMIFPDWAV 363
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 32.3 bits (72), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 37/95 (38%), Gaps = 18/95 (18%)
Query: 299 DGLHFMGRDITFQNTAGPL----KGQAVALRSASDLSVFYRCAFQGYQDTLMVHSQ---- 350
+GL +++T +NT G AVALR+ D G Q+T V +
Sbjct: 201 NGLQL--QNLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQN 258
Query: 351 --------RQFYKKCYIYGTIDFIFGNAAVVFQNC 377
R YI G +D + G AVVF N
Sbjct: 259 RLETNRQPRTLVTNSYIEGDVDIVSGRGAVVFDNT 293
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 208 SLEARANLVVATDGSGN--YRTIQAAINAAAGRRGSGRFIIHVKRGVYRENIEVGLNNNN 265
+L A+ + VV G+ + TIQAA++AA +R + R I V G Y+ + V
Sbjct: 70 TLPAQPDFVVGPAGTQGVTHTTIQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGG 129
Query: 266 IMLVGEGMR 274
I L G G +
Sbjct: 130 ITLYGTGEK 138
>pdb|3RJ1|E Chain E, Architecture Of The Mediator Head Module
pdb|3RJ1|L Chain L, Architecture Of The Mediator Head Module
pdb|3RJ1|S Chain S, Architecture Of The Mediator Head Module
Length = 275
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 127 TDFDAQTWLSTALTNIRTCQSGYMELNVSD 156
TD D + TAL N++ GY+EL+V D
Sbjct: 231 TDIDRINYTETALXNLKKELQGYIELSVPD 260
>pdb|4GWP|E Chain E, Structure Of The Mediator Head Module From S. Cerevisiae
pdb|4GWQ|E Chain E, Structure Of The Mediator Head Module From S. Cerevisiae
In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
Polymerase Ii Rpb1 Subunit
Length = 307
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 127 TDFDAQTWLSTALTNIRTCQSGYMELNVSD 156
TD D + TAL N++ GY+EL+V D
Sbjct: 263 TDIDRINYTETALMNLKKELQGYIELSVPD 292
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
0.321 0.135 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,553,816
Number of Sequences: 62578
Number of extensions: 571265
Number of successful extensions: 1073
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1052
Number of HSP's gapped (non-prelim): 18
length of query: 528
length of database: 14,973,337
effective HSP length: 103
effective length of query: 425
effective length of database: 8,527,803
effective search space: 3624316275
effective search space used: 3624316275
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)