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= 008485
(564 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 351 bits (900), Expect = 7e-97, Method: Compositional matrix adjust.
Identities = 170/312 (54%), Positives = 211/312 (67%), Gaps = 3/312 (0%)
Query: 252 VSQDGSGNFTTITDAINVAPNNTDVTNGYFLIYITAGVYEEYISISKNKKNLMIIGDGIN 311
V+QDG+G++ T+ +A+ AP+ + ++IY+ G Y+E + ++ NK NLMI+GDG+
Sbjct: 7 VAQDGTGDYQTLAEAVAAAPDKSKTR---YVIYVKRGTYKENVEVASNKMNLMIVGDGMY 63
Query: 312 QTVITGNRSVVDGWTTFNSATFAVVAPKFVAVNITIRNTAGAIKHQAVALRNGADLSTFY 371
T ITG+ +VVDG TTF SAT A V F+ +I I+NTAG K QAVALR GAD+S
Sbjct: 64 ATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVIN 123
Query: 372 SCSFEAYQDTLYTHSLRQFYRECDIYGTVDFIFGNAAVVLQNCNIYPRLPMSGQFNAITA 431
C +AYQDTLY HS RQFYR+ + GTVDFIFGNAAVV Q C + R P Q N +TA
Sbjct: 124 RCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTA 183
Query: 432 QGRTDPNQNTGTSIHNCTIRASSDLASGSQTVQTYLGRPWKEYSRTVYMQSFMDSSINPA 491
QGRTDPNQ TGTSI C I ASSDL + TYLGRPWKEYSRTV M+S++ INPA
Sbjct: 184 QGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPA 243
Query: 492 GWQIWSGDFALSTLYYAEYNNTGPGSNTANRVTWPGYHVTINATDAANFTVSNFLLGDDW 551
GW W GDFAL TLYY E+ N GPG+ T+ RV WPGYHV + A FTV+ + G W
Sbjct: 244 GWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSW 303
Query: 552 IPQTGVSYTGAL 563
+ TGV+Y L
Sbjct: 304 LRSTGVAYVDGL 315
>pdb|1GQ8|A Chain A, Pectin Methylesterase From Carrot
Length = 319
Score = 350 bits (897), Expect = 2e-96, Method: Compositional matrix adjust.
Identities = 172/306 (56%), Positives = 215/306 (70%), Gaps = 3/306 (0%)
Query: 250 VTVSQDGSGNFTTITDAINVAPNNTDVTNGYFLIYITAGVYEEYISISKNKKNLMIIGDG 309
V V+ DGSG++ T+++A+ AP ++ ++I I AGVY E + + K KKN+M +GDG
Sbjct: 9 VVVAADGSGDYKTVSEAVAAAPEDSKTR---YVIRIKAGVYRENVDVPKKKKNIMFLGDG 65
Query: 310 INQTVITGNRSVVDGWTTFNSATFAVVAPKFVAVNITIRNTAGAIKHQAVALRNGADLST 369
T+IT +++V DG TTFNSAT A V F+A +IT +NTAGA KHQAVALR G+DLS
Sbjct: 66 RTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSA 125
Query: 370 FYSCSFEAYQDTLYTHSLRQFYRECDIYGTVDFIFGNAAVVLQNCNIYPRLPMSGQFNAI 429
FY C AYQD+LY HS RQF+ C I GTVDFIFGNAAVVLQ+C+I+ R P SGQ N +
Sbjct: 126 FYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMV 185
Query: 430 TAQGRTDPNQNTGTSIHNCTIRASSDLASGSQTVQTYLGRPWKEYSRTVYMQSFMDSSIN 489
TAQGRTDPNQNTG I I A+SDL + TYLGRPWKEYSRTV MQS + + IN
Sbjct: 186 TAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVIN 245
Query: 490 PAGWQIWSGDFALSTLYYAEYNNTGPGSNTANRVTWPGYHVTINATDAANFTVSNFLLGD 549
PAGW W G+FAL TLYY EY NTG G+ T+ RVTW G+ V ++T+A FT +F+ G
Sbjct: 246 PAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGG 305
Query: 550 DWIPQT 555
W+ T
Sbjct: 306 SWLKAT 311
>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 = 103 bits (258), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 108/353 (30%), Positives = 150/353 (42%), Gaps = 68/353 (19%)
Query: 249 IVTVSQDGSGNFTTITDAINVAPNNTDVTNGYFLIYITAGVYEEYISISKNKKNLMIIGD 308
+V+ S F TI DAI AP + F+I I GVY E ++I++N NL + G+
Sbjct: 7 VVSKSSSDGKTFKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGE 60
Query: 309 GINQTVITGN------RSVVDGWTTFNSATFAVVAPKFVAVNITIRNT------------ 350
N VI +S W T S+T + A F A ++TIRN
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 351 -AGAIKH-QAVAL--RNGADLSTFYSCSFEAYQDTLYTHSLRQFYRECDIYGTVDFIFGN 406
+ IK QAVAL D + F S YQDTLY R F+ +C I GTVDFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 407 AAVVLQNCNIYPRLPM---SGQFNAITAQGRTDPNQNTGTSIHNCTIRASSDLASGSQTV 463
+ NC++ R SG + T+ NQ G I N + SD S
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESD----SVPA 236
Query: 464 QTY-LGRPWK--------------EYSRTVYMQSFMDSSINPAGWQIWSG-DFALSTLYY 507
++Y LGRPW +TV++ + MD+ I GW SG D +T+++
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 508 A-------EYNNTGPGSNTANRVTWPGYHVTINATDAANFTVSNFLLGDDWIP 553
EY + G G+ + + AA +T S L DW P
Sbjct: 295 NPEDSRFFEYKSYGAGATVSKD------RRQLTDAQAAEYTQSKVL--GDWTP 339
>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 (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 108/353 (30%), Positives = 150/353 (42%), Gaps = 68/353 (19%)
Query: 249 IVTVSQDGSGNFTTITDAINVAPNNTDVTNGYFLIYITAGVYEEYISISKNKKNLMIIGD 308
+V+ S F TI DAI AP + F+I I GVY E ++I++N NL + G+
Sbjct: 7 VVSKSSSDGKTFKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGE 60
Query: 309 GINQTVITGN------RSVVDGWTTFNSATFAVVAPKFVAVNITIRNT------------ 350
N VI +S W T S+T + A F A ++TIRN
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 351 -AGAIKH-QAVAL--RNGADLSTFYSCSFEAYQDTLYTHSLRQFYRECDIYGTVDFIFGN 406
+ IK QAVAL D + F S YQDTLY R F+ +C I GTVDFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 407 AAVVLQNCNIYPRLPM---SGQFNAITAQGRTDPNQNTGTSIHNCTIRASSDLASGSQTV 463
+ NC++ R SG + T+ NQ G I N + SD S
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESD----SVPA 236
Query: 464 QTY-LGRPWK--------------EYSRTVYMQSFMDSSINPAGWQIWSG-DFALSTLYY 507
++Y LGRPW +TV++ + MD+ I GW SG D +T+++
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 508 A-------EYNNTGPGSNTANRVTWPGYHVTINATDAANFTVSNFLLGDDWIP 553
EY + G G+ + + AA +T S L DW P
Sbjct: 295 NPEDSRFFEYKSYGAGAAVSKD------RRQLTDAQAAEYTQSKVL--GDWTP 339
>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 = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 107/353 (30%), Positives = 149/353 (42%), Gaps = 68/353 (19%)
Query: 249 IVTVSQDGSGNFTTITDAINVAPNNTDVTNGYFLIYITAGVYEEYISISKNKKNLMIIGD 308
+V+ S F TI DAI AP + F+I I GVY E ++I++N NL + G+
Sbjct: 7 VVSKSSSDGKTFKTIADAIASAPAGSTP----FVILIKNGVYNERLTITRN--NLHLKGE 60
Query: 309 GINQTVITGN------RSVVDGWTTFNSATFAVVAPKFVAVNITIRNT------------ 350
N VI +S W T S+T + A F A ++TIRN
Sbjct: 61 SRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDS 120
Query: 351 -AGAIKH-QAVAL--RNGADLSTFYSCSFEAYQDTLYTHSLRQFYRECDIYGTVDFIFGN 406
+ IK QAVAL D + F S YQ TLY R F+ +C I GTVDFIFG+
Sbjct: 121 DSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGD 180
Query: 407 AAVVLQNCNIYPRLPM---SGQFNAITAQGRTDPNQNTGTSIHNCTIRASSDLASGSQTV 463
+ NC++ R SG + T+ NQ G I N + SD S
Sbjct: 181 GTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESD----SVPA 236
Query: 464 QTY-LGRPWK--------------EYSRTVYMQSFMDSSINPAGWQIWSG-DFALSTLYY 507
++Y LGRPW +TV++ + MD+ I GW SG D +T+++
Sbjct: 237 KSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHI--YGWDKMSGKDKNGNTIWF 294
Query: 508 A-------EYNNTGPGSNTANRVTWPGYHVTINATDAANFTVSNFLLGDDWIP 553
EY + G G+ + + AA +T S L DW P
Sbjct: 295 NPEDSRFFEYKSYGAGATVSKD------RRQLTDAQAAEYTQSKVL--GDWTP 339
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 91.7 bits (226), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 90/316 (28%), Positives = 138/316 (43%), Gaps = 61/316 (19%)
Query: 249 IVTVSQDGSGNFTTITDAINVAPNNTDVTNGYFLIYITAGVYEEYISISKNKKNLMIIGD 308
+V+ + G F++I A+ AP + + F+I++ GVY E + ++++ ++ + G+
Sbjct: 34 VVSTTPQGD-EFSSINAALKSAPKD----DTPFIIFLKNGVYTERLEVARS--HVTLKGE 86
Query: 309 GINQTVITGNRSVV------DGWTTFNSATFAVVAPKFVAVNITIRNT----AGAIKH-- 356
+ TVI N + + W T S+T V AP F A N+TIRN A K
Sbjct: 87 NRDGTVIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADT 146
Query: 357 --------QAVAL--RNGADLSTFYSCSFEAYQDTLYTHS-LRQFYRECDIYGTVDFIFG 405
QAVAL +D + F + E YQDTLY+ + R ++ +C+I G VDFIFG
Sbjct: 147 DPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFG 206
Query: 406 NAAVVLQNCNIYP--RLPMSGQFNAITAQGRTDPNQNTGTSIHNCTIRASSDLASGSQTV 463
+ V NCNI R + + ITA P+ T + I + G
Sbjct: 207 SGITVFDNCNIVARDRSDIEPPYGYITA-----PSTLTTSPYGLIFINSRLTKEPGVPAN 261
Query: 464 QTYLGRPWKE--------------YSRTVYMQSFMDSSINPAGWQIWSGD--------FA 501
LGRPW ++V++ + MD I GW SG F
Sbjct: 262 SFALGRPWHPTTTFADGRYADPAAIGQSVFINTTMDDHI--YGWDKMSGKDKQGEKIWFY 319
Query: 502 LSTLYYAEYNNTGPGS 517
+ E N+ GPG+
Sbjct: 320 PQDSRFFEANSQGPGA 335
>pdb|4E2K|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
pdb|4EDG|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Atp And Manganese
pdb|4EDK|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Gtp And Manganese
pdb|4EDR|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Utp And Manganese
pdb|4EDT|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ppgpp And Manganese
pdb|4EDV|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Pppgpp And Manganese
pdb|4EE1|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ctp And Manganese
Length = 329
Score = 36.6 bits (83), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 74 LWQSRKFLNLVDKYLTRRATLSTTAIRALEDCRLLAGFNMDFLLSSFETVNSTSKTLPTM 133
++Q RK L +DK + +IR L++ LL GF MD + S + + T+ T
Sbjct: 132 IFQKRKLLYNLDK--------ARKSIRKLDEIVLLEGF-MDVIKSDTAGLKNVVATMGTQ 182
Query: 134 QADDVQTFLSAILTNQQTCFDG 155
+D+ TF+ + +N FDG
Sbjct: 183 LSDEHITFIRKLTSNITLMFDG 204
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 37/86 (43%), Gaps = 16/86 (18%)
Query: 344 NITIRNTAG----AIKHQAVALRNGADLSTFYSCSFEAYQDTLY-THSLRQFYRECD--- 395
N+TI NT G A H AVALR D + + Q+T + T+S Q E +
Sbjct: 207 NLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQP 266
Query: 396 --------IYGTVDFIFGNAAVVLQN 413
I G VD + G AVV N
Sbjct: 267 RTLVTNSYIEGDVDIVSGRGAVVFDN 292
>pdb|3HRK|A Chain A, Histidyl-Trna Synthetase From Trypanosoma Cruzi
(Histidyl-Adenylate Complex)
pdb|3HRK|B Chain B, Histidyl-Trna Synthetase From Trypanosoma Cruzi
(Histidyl-Adenylate Complex)
pdb|3LC0|A Chain A, Histidyl-Trna Synthetase From Trypanosoma Cruzi (Histidine
Complex)
Length = 456
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 386 SLRQFYRECDIYGTVDFIFGNAAVV----LQNCNIYPRLPMSGQFNAITAQGRTD 436
LRQF+ + + YG D++ +A+VV ++ G+F A+ GR D
Sbjct: 267 ELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYD 321
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
0.319 0.131 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,541,450
Number of Sequences: 62578
Number of extensions: 687076
Number of successful extensions: 1409
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1392
Number of HSP's gapped (non-prelim): 10
length of query: 564
length of database: 14,973,337
effective HSP length: 104
effective length of query: 460
effective length of database: 8,465,225
effective search space: 3894003500
effective search space used: 3894003500
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: 54 (25.4 bits)