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= 039481
(229 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 = 168 bits (425), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 94/238 (39%), Positives = 129/238 (54%), Gaps = 17/238 (7%)
Query: 4 GKGDFKKIQDAIDSVPSNNSETVFIRVKPGTYREKIAVPADKPFITISGTKASSTIITWS 63
G GD+K + +A+ + P ++ IR+K G YRE + VP K I G +STIIT S
Sbjct: 15 GSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTIITAS 74
Query: 64 ----DGGEIFESATFTVLADDFVGRFLTIENTYGSAG-KAVALRVSADRAAFYGCRILSY 118
DG F SAT + F+ R +T +NT G+A +AVALRV +D +AFY C IL+Y
Sbjct: 75 KNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYRCDILAY 134
Query: 119 QDTLLDDTGNHYYCNCYIEGATDFICGDAASLFESCHIHSLSTGNG---AITAQKRVLPE 175
QD+L + ++ NC+I G DFI G+AA + + C IH+ G+G +TAQ R P
Sbjct: 135 QDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQGRTDPN 194
Query: 176 ENTGINFLGCKITGVG---------KAVLGRPWGTYSRVVYALTYMSGVIQPPGWDDW 224
+NTGI +I LGRPW YSR V + ++ VI P GW W
Sbjct: 195 QNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAGWFPW 252
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 148 bits (373), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 86/240 (35%), Positives = 123/240 (51%), Gaps = 17/240 (7%)
Query: 2 QSGKGDFKKIQDAIDSVPSNNSETVFIRVKPGTYREKIAVPADKPFITISGTKASSTIIT 61
Q G GD++ + +A+ + P + I VK GTY+E + V ++K + I G +T IT
Sbjct: 9 QDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTIT 68
Query: 62 WS----DGGEIFESATFTVLADDFVGRFLTIENTYGSAG-KAVALRVSADRAAFYGCRIL 116
S DG F SAT + F+ + + I+NT G A +AVALRV AD + CRI
Sbjct: 69 GSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRID 128
Query: 117 SYQDTLLDDTGNHYYCNCYIEGATDFICGDAASLFESCHIHSLSTG---NGAITAQKRVL 173
+YQDTL + +Y + Y+ G DFI G+AA +F+ C + + G +TAQ R
Sbjct: 129 AYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTD 188
Query: 174 PEENTGINFLGCKITGVG---------KAVLGRPWGTYSRVVYALTYMSGVIQPPGWDDW 224
P + TG + C I LGRPW YSR V +Y+ G+I P GW +W
Sbjct: 189 PNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEW 248
>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 = 71.6 bits (174), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 68/230 (29%), Positives = 102/230 (44%), Gaps = 40/230 (17%)
Query: 8 FKKIQDAIDSVPSNNSETVFIRVKPGTYREKIAVPADKPFI------TISGTKASSTIIT 61
FK I DAI S P+ ++ V I +K G Y E++ + + + A++
Sbjct: 18 FKTIADAIASAPAGSTPFV-ILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 62 WSDGGE--IFESATFTVLADDFVGRFLTIENTYGSAG---------------KAVALRV- 103
SDG + S+T T+ A DF + LTI N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 104 -SADRAAFYGCRILSYQDTLLDDTGNHYYCNCYIEGATDFICGDAASLFESCHIHS---- 158
S DRA F ++ YQDTL G ++ +C I G DFI GD +LF +C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 159 -LSTGN--GAITAQKRVLPEENTGINFLGCKITGVGKAV------LGRPW 199
+ +GN G +TA + + G+ ++ +V LGRPW
Sbjct: 197 DVKSGNVSGYLTAPSTNI-NQKYGLVITNSRVIRESDSVPAKSYGLGRPW 245
>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 = 71.6 bits (174), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 68/230 (29%), Positives = 102/230 (44%), Gaps = 40/230 (17%)
Query: 8 FKKIQDAIDSVPSNNSETVFIRVKPGTYREKIAVPADKPFI------TISGTKASSTIIT 61
FK I DAI S P+ ++ V I +K G Y E++ + + + A++
Sbjct: 18 FKTIADAIASAPAGSTPFV-ILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 62 WSDGGE--IFESATFTVLADDFVGRFLTIENTYGSAG---------------KAVALRV- 103
SDG + S+T T+ A DF + LTI N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 104 -SADRAAFYGCRILSYQDTLLDDTGNHYYCNCYIEGATDFICGDAASLFESCHIHS---- 158
S DRA F ++ YQDTL G ++ +C I G DFI GD +LF +C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 159 -LSTGN--GAITAQKRVLPEENTGINFLGCKITGVGKAV------LGRPW 199
+ +GN G +TA + + G+ ++ +V LGRPW
Sbjct: 197 DVKSGNVSGYLTAPSTNI-NQKYGLVITNSRVIRESDSVPAKSYGLGRPW 245
>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 = 68.6 bits (166), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 67/230 (29%), Positives = 101/230 (43%), Gaps = 40/230 (17%)
Query: 8 FKKIQDAIDSVPSNNSETVFIRVKPGTYREKIAVPADKPFI------TISGTKASSTIIT 61
FK I DAI S P+ ++ V I +K G Y E++ + + + A++
Sbjct: 18 FKTIADAIASAPAGSTPFV-ILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTL 76
Query: 62 WSDGGE--IFESATFTVLADDFVGRFLTIENTYGSAG---------------KAVALRV- 103
SDG + S+T T+ A DF + LTI N + +AVAL V
Sbjct: 77 KSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVT 136
Query: 104 -SADRAAFYGCRILSYQDTLLDDTGNHYYCNCYIEGATDFICGDAASLFESCHIHS---- 158
S DRA F ++ YQ TL G ++ +C I G DFI GD +LF +C + S
Sbjct: 137 KSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRA 196
Query: 159 -LSTGN--GAITAQKRVLPEENTGINFLGCKITGVGKAV------LGRPW 199
+ +GN G +TA + + G+ ++ +V LGRPW
Sbjct: 197 DVKSGNVSGYLTAPSTNI-NQKYGLVITNSRVIRESDSVPAKSYGLGRPW 245
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 68.6 bits (166), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 64/231 (27%), Positives = 103/231 (44%), Gaps = 42/231 (18%)
Query: 7 DFKKIQDAIDSVPSNNSETVFIRVKPGTYREKIAVPADKPFITISGTKASSTIITWSDGG 66
+F I A+ S P +++ + I +K G Y E++ V + +T+ G T+I +
Sbjct: 43 EFSSINAALKSAPKDDTPFI-IFLKNGVYTERLEVA--RSHVTLKGENRDGTVIGANTAA 99
Query: 67 EIFE----------SATFTVLADDFVGRFLTIENTYGSAG---------------KAVAL 101
+ S+T V A +F LTI N + +AVAL
Sbjct: 100 GMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPANKKKADTDPTKLKDTQAVAL 159
Query: 102 RVS--ADRAAFYGCRILSYQDTLLDDTGNH-YYCNCYIEGATDFICGDAASLFESCHIHS 158
++ +D+A F ++ YQDTL TG+ Y+ +C I G DFI G ++F++C+I +
Sbjct: 160 LLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGHVDFIFGSGITVFDNCNIVA 219
Query: 159 LSTGN-----GAITAQKRVLPEENTGINFLGCKIT---GV--GKAVLGRPW 199
+ G ITA L G+ F+ ++T GV LGRPW
Sbjct: 220 RDRSDIEPPYGYITAPS-TLTTSPYGLIFINSRLTKEPGVPANSFALGRPW 269
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 50/209 (23%), Positives = 73/209 (34%), Gaps = 58/209 (27%)
Query: 11 IQDAIDS-VPSNNSETVFIRVKPGTYREKIAVPADKPFITISGTKASSTII--------- 60
IQ A+D+ + ++ +I V PG Y+ + VPA IT+ GT +
Sbjct: 92 IQAAVDAAIIKRTNKRQYIAVMPGEYQGTVYVPAAPGGITLYGTGEKPIDVKIGLSLDGG 151
Query: 61 ---------------------TW----------SDGGEIFESATFTVLADDFVGRFLTIE 89
W SD + SA F + + LTIE
Sbjct: 152 MSPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLCSAVFWSQNNGLQLQNLTIE 211
Query: 90 NTYGS---AGK--AVALRVSADRAAFYGCRILSYQDTLL------------DDTGNHYYC 132
NT G AG AVALR D+ IL Q+T +
Sbjct: 212 NTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVTNSGVQNRLETNRQPRTLVT 271
Query: 133 NCYIEGATDFICGDAASLFESCHIHSLST 161
N YIEG D + G A +F++ +++
Sbjct: 272 NSYIEGDVDIVSGRGAVVFDNTEFRVVNS 300
>pdb|3NTK|A Chain A, Crystal Structure Of Tudor
pdb|3NTK|B Chain B, Crystal Structure Of Tudor
Length = 169
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 154 CHIHSLSTGNGAITAQKRVLPEE 176
C +H + GN A+T Q R LPEE
Sbjct: 78 CEVHFIDFGNNAVTQQFRQLPEE 100
>pdb|3NTH|A Chain A, Crystal Structure Of Tudor And Aubergine [r13(Me2s)]
Complex
pdb|3NTI|A Chain A, Crystal Structure Of Tudor And Aubergine [r15(Me2s)]
Complex
Length = 172
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 153 SCHIHSLSTGNGAITAQKRVLPEE 176
C +H + GN A+T Q R LPEE
Sbjct: 79 KCEVHFIDFGNNAVTQQFRQLPEE 102
>pdb|1J4E|A Chain A, Fructose-1,6-Bisphosphate Aldolase Covalently Bound To The
Substrate Dihydroxyacetone Phosphate
pdb|1J4E|B Chain B, Fructose-1,6-Bisphosphate Aldolase Covalently Bound To The
Substrate Dihydroxyacetone Phosphate
pdb|1J4E|C Chain C, Fructose-1,6-Bisphosphate Aldolase Covalently Bound To The
Substrate Dihydroxyacetone Phosphate
pdb|1J4E|D Chain D, Fructose-1,6-Bisphosphate Aldolase Covalently Bound To The
Substrate Dihydroxyacetone Phosphate
Length = 363
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 12/55 (21%)
Query: 166 ITAQKRVLPEENTGINFL---------GCKITGVGKAVLGRPWG---TYSRVVYA 208
+TA +R +P TG+ FL + + KA L +PW +Y R + A
Sbjct: 253 VTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKAPLLKPWALTFSYGRALQA 307
>pdb|1GOZ|A Chain A, Structural Basis For The Altered T-Cell Receptor Binding
Specificty In A Superantigenic Staphylococcus Aureus
Enterotoxin-B Mutant
pdb|1GOZ|B Chain B, Structural Basis For The Altered T-Cell Receptor Binding
Specificty In A Superantigenic Staphylococcus Aureus
Enterotoxin-B Mutant
Length = 239
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 2/90 (2%)
Query: 117 SYQDTLLDDTGNHYYCNCYIEGATDFICGDAASLFESCHIHSLSTGNGAITAQKRVLPEE 176
Y+D +D G +YY CY T+ I +SC ++ NG + R +
Sbjct: 76 KYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKSCMYGGVTEHNGNQLDKYRSITVR 135
Query: 177 --NTGINFLGCKITGVGKAVLGRPWGTYSR 204
G N L + K V + +R
Sbjct: 136 VFEDGKNLLSFDVQTNKKKVTAQELDYLTR 165
>pdb|3GP7|A Chain A, Staphylococcal Enterotoxin B Mutant N23yk97sk98s
pdb|3GP7|B Chain B, Staphylococcal Enterotoxin B Mutant N23yk97sk98s
Length = 239
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 2/90 (2%)
Query: 117 SYQDTLLDDTGNHYYCNCYIEGATDFICGDAASLFESCHIHSLSTGNGAITAQKRVLPEE 176
Y+D +D G +YY CY +T+ I ++C ++ NG + R +
Sbjct: 76 KYKDKYVDVFGANYYYQCYFSSSTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVR 135
Query: 177 --NTGINFLGCKITGVGKAVLGRPWGTYSR 204
G N L + K V + +R
Sbjct: 136 VFEDGKNLLSFDVQTNKKKVTAQELDYLTR 165
>pdb|1NCF|A Chain A, A New Paradigm For Tumor Necrosis Factor Signalling
pdb|1NCF|B Chain B, A New Paradigm For Tumor Necrosis Factor Signalling
pdb|1EXT|A Chain A, Extracellular Domain Of The 55kda Tumor Necrosis Factor
Receptor. Crystallized At Ph3.7 In P 21 21 21.
pdb|1EXT|B Chain B, Extracellular Domain Of The 55kda Tumor Necrosis Factor
Receptor. Crystallized At Ph3.7 In P 21 21 21.
pdb|1FT4|A Chain A, Photochemically-Enhanced Binding Of Small Molecules To The
Tumor Necrosis Factor Receptor-1
pdb|1FT4|B Chain B, Photochemically-Enhanced Binding Of Small Molecules To The
Tumor Necrosis Factor Receptor-1
Length = 162
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 22/115 (19%), Positives = 42/115 (36%), Gaps = 10/115 (8%)
Query: 70 ESATFTVLADDFVGRFLTIENTYGSAGKAVALRVSADRAAFYGCRILSYQDTLLDDTGNH 129
ES +FT +++ + L+ G+ + DR GCR Y+ ++
Sbjct: 46 ESGSFTA-SENHLRHCLSCSKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQC 104
Query: 130 YYCNCYIEGATDFICGDAASLFESCH---------IHSLSTGNGAITAQKRVLPE 175
+ C+ + G C + + +CH S S ++ K LP+
Sbjct: 105 FNCSLCLNGTVHLSCQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQ 159
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 0.136 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,542,319
Number of Sequences: 62578
Number of extensions: 314320
Number of successful extensions: 787
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 744
Number of HSP's gapped (non-prelim): 33
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)