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= 012788
(456 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JUR|A Chain A, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|B Chain B, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|C Chain C, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
pdb|3JUR|D Chain D, The Crystal Structure Of A Hyperthermoactive
Exopolygalacturonase From Thermotoga Maritima
Length = 448
Score = 110 bits (274), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 92/339 (27%), Positives = 145/339 (42%), Gaps = 49/339 (14%)
Query: 39 HSVSITEFGAVGDGKTLNTLAFQNAIFYLKSFADKGGAQLYVPSGKWLTGSFNLTSHLTL 98
V++ +FGA GDG+T + +F+ AI + + +GG +L VP G +LTG +L S++ L
Sbjct: 26 REVNLLDFGARGDGRTDCSESFKRAI---EELSKQGGGRLIVPEGVFLTGPIHLKSNIEL 82
Query: 99 FLEKGAVILGSQNPSHWDVVDPLPSYGRGIELPGRRYKSLINGYMLRDVVVTGDNGTIDG 158
+ KG + + VV L + GIEL Y L+ +V +TG +G +DG
Sbjct: 83 HV-KGTIKFIPDPERYLPVV--LTRF-EGIEL--YNYSPLVYALDCENVAITG-SGVLDG 135
Query: 159 QG--SVWWDWFSSQSL----------------------------------NYSRPHLVEF 182
WW W + +Y RP V+F
Sbjct: 136 SADNEHWWPWKGKKDFGWKEGLPNQQEDVKKLKEMAERGTPVEERVFGKGHYLRPSFVQF 195
Query: 183 ISSENVVVSNLTFLNAPAYNIHPVYCSNVHIQNISVHAPPESPYTVGIVPDSSDNVCIED 242
NV+V + +N+P + IHPV NV I+NI + + P GI P+S + IE
Sbjct: 196 YRCRNVLVEGVKIINSPMWCIHPVLSENVIIRNIEISST--GPNNDGIDPESCKYMLIEK 253
Query: 243 CIIAMGHDAISLKSGWDEYGIAYGRPTTDVHIR-RVLLQXXXXXXXXXXXXXXGGISNVQ 301
C G D++ +KSG D G G P+ + +R +++ GG+ NV
Sbjct: 254 CRFDTGDDSVVIKSGRDADGRRIGVPSEYILVRDNLVISQASHGGLVIGSEMSGGVRNVV 313
Query: 302 VEKIHLYDSLNGIEFRTTKGRGGYIRQIVISDAELYNIN 340
+ + +T RGGY+ I D N++
Sbjct: 314 ARNNVYMNVERALRLKTNSRRGGYMENIFFIDNVAVNVS 352
>pdb|2UVE|A Chain A, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase
pdb|2UVE|B Chain B, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase
pdb|2UVF|A Chain A, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase In Complex With Digalaturonic Acid
pdb|2UVF|B Chain B, Structure Of Yersinia Enterocolitica Family 28
Exopolygalacturonase In Complex With Digalaturonic Acid
Length = 608
Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 55/162 (33%), Positives = 86/162 (53%), Gaps = 21/162 (12%)
Query: 37 RPHSVSITEFGAVGDGKTLNTLAFQNAIFYLKSFADKGGAQLYVPSGKWLTGSFNLTSHL 96
+P V++ +FGA+ DGKTLNT A Q AI K G ++ +P+G + +G+ L S +
Sbjct: 153 KPQIVNVRDFGAIDDGKTLNTKAIQQAIDSCKP-----GCRVEIPAGTYKSGALWLKSDM 207
Query: 97 TLFLEKGAVILGSQNPSHWDVVDPLPSYGRGIELPGRRYKSLINGY--------MLRDVV 148
TL L+ GA++LGS+NP + L Y IE P SLIN R++
Sbjct: 208 TLNLQAGAILLGSENPDDYPAGYRLYPYST-IERPA----SLINAIDPNNSKPGTFRNIR 262
Query: 149 VTGDNGTIDGQGSVWWDWFSSQSLNYSRPHLVEFISSENVVV 190
+TG +G IDG G W +++ + L ++++S+N V
Sbjct: 263 ITG-SGVIDGNG--WLRAKTAEITDELGRSLPQYVASKNSKV 301
>pdb|1BHE|A Chain A, Polygalacturonase From Erwinia Carotovora Ssp. Carotovora
Length = 376
Score = 65.1 bits (157), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 64/269 (23%), Positives = 114/269 (42%), Gaps = 30/269 (11%)
Query: 85 WLTGSFNLTSHLTLFLEKGAVILGSQNPSHWDVVDPLPSYGRGIELPGRRYKSLINGYML 144
+L+G +L S ++L ++KG + N ++ PS ++ G+ + I
Sbjct: 52 FLSGPLSLPSGVSLLIDKGVTLRAVNNAKSFE---NAPSSCGVVDKNGKGCDAFITAVST 108
Query: 145 RDVVVTGDNGTIDGQGSV--------WWDWFSS---QSLNYSRPHLVEFISSENVVVSNL 193
+ + G GTIDGQG V WW+ + + L + P L++ S+N + N+
Sbjct: 109 TNSGIYGP-GTIDGQGGVKLQDKKVSWWELAADAKVKKLKQNTPRLIQINKSKNFTLYNV 167
Query: 194 TFLNAPAYNIHPVYCSNVHIQ--NISVHAPPESPYTVGIVPDSSDNVCIEDCIIAMGHDA 251
+ +N+P N H V+ ++ P + T GI P SS N+ I IA G D
Sbjct: 168 SLINSP--NFHVVFSDGDGFTAWKTTIKTPSTARNTDGIDPMSSKNITIAYSNIATGDDN 225
Query: 252 ISLKSGWDEYGIAY-GRPTTDVHIRRVLLQXXXXXXXXXXXXXXGGISNVQVEKIHLYDS 310
+++K AY GR T +L G+ NV V+ + + +
Sbjct: 226 VAIK--------AYKGRAET--RNISILHNDFGTGHGMSIGSETMGVYNVTVDDLKMNGT 275
Query: 311 LNGIEFRTTKGRGGYIRQIVISDAELYNI 339
NG+ ++ K G + + S+ + N+
Sbjct: 276 TNGLRIKSDKSAAGVVNGVRYSNVVMKNV 304
>pdb|2VBE|A Chain A, Tailspike Protein Of Bacteriophage Sf6
Length = 514
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 37/119 (31%), Positives = 52/119 (43%), Gaps = 10/119 (8%)
Query: 35 DPRPHSVSITEFGAVGDGKTLNTLAFQNAIFYLKSFADKGGAQLYVPSGKWLTGSFNLTS 94
D ++SI +FG + DG T N A QNAI + S G +L++P+ G +
Sbjct: 46 DKNKEAISILDFGVIDDGVTDNYQAIQNAIDAVASLPS--GGELFIPASNQAVGYIVGS- 102
Query: 95 HLTLFLEKGAVILGSQNPSHWDVVDPLPSYGRGIELPGRRYKSLINGYMLRDVVVTGDN 153
TL + G I G S L G + L Y S G LR++ VTG+N
Sbjct: 103 --TLLIPGGVNIRGVGKASQLRAKSGLT--GSVLRLS---YDSDTIGRYLRNIRVTGNN 154
>pdb|2VBK|A Chain A, Native Tailspike Protein Of Bacteriophage Sf6
pdb|2VBM|A Chain A, Tailspike Protein Of Bacteriophage Sf6 Complexed With
Tetrasaccharide
Length = 514
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 37/119 (31%), Positives = 52/119 (43%), Gaps = 10/119 (8%)
Query: 35 DPRPHSVSITEFGAVGDGKTLNTLAFQNAIFYLKSFADKGGAQLYVPSGKWLTGSFNLTS 94
D ++SI +FG + DG T N A QNAI + S G +L++P+ G +
Sbjct: 46 DKNKEAISILDFGVIDDGVTDNYQAIQNAIDAVASLPS--GGELFIPASNQAVGYIVGS- 102
Query: 95 HLTLFLEKGAVILGSQNPSHWDVVDPLPSYGRGIELPGRRYKSLINGYMLRDVVVTGDN 153
TL + G I G S L G + L Y S G LR++ VTG+N
Sbjct: 103 --TLLIPGGVNIRGVGKASQLRAKSGLT--GSVLRLS---YDSDTIGRYLRNIRVTGNN 154
>pdb|1NHC|A Chain A, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|B Chain B, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|C Chain C, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|D Chain D, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|E Chain E, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|F Chain F, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
Length = 336
Score = 36.2 bits (82), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 133 RRYKSLINGYMLRDVVVT-GDNGTIDGQGSVWWDWFSSQSLN--YSRPHLVEFISSENVV 189
+ +K + + +D+ VT D IDG GS WWD S+ N ++P + E+
Sbjct: 56 KEWKGPLIRFGGKDLTVTMADGAVIDGDGSRWWD---SKGTNGGKTKPKFMYIHDVEDST 112
Query: 190 VSNLTFLNAPAYNIHPVYCSNVHIQNISV 218
+ N P I V +NVH+ + ++
Sbjct: 113 FKGINIKNTPVQAI-SVQATNVHLNDFTI 140
>pdb|1K5C|A Chain A, Endopolygalacturonase I From Stereum Purpureum At 0.96 A
Resolution
pdb|1KCC|A Chain A, Endopolygalacturonase I From Stereum Purpureum Complexed
With A Galacturonate At 1.00 A Resolution.
pdb|1KCD|A Chain A, Endopolygalacturonase I From Stereum Purpureum Complexed
With Two Galacturonate At 1.15 A Resolution
Length = 335
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 61/140 (43%), Gaps = 19/140 (13%)
Query: 157 DGQGSVWWDWFSSQSLNYSRPHLVEFISSENVVVSNLTFLNAPAYNIHPVYCSNVHI--Q 214
DG G+++WD + + + +PH I LN+PA I V ++ H+
Sbjct: 78 DGNGALYWDGKGTNNGTH-KPHPFLKIKGSGTY-KKFEVLNSPAQAI-SVGPTDAHLTLD 134
Query: 215 NISVHAPPESPYTVGIVPD----SSDNVCIEDCIIAMGHDAISLKSGWD----------E 260
I+V +G D S++NV I++CI+ D I++ G +
Sbjct: 135 GITVDDFAGDTKNLGHNTDGFDVSANNVTIQNCIVKNQDDCIAINDGNNIRFENNQCSGG 194
Query: 261 YGIAYGRPTTDVHIRRVLLQ 280
+GI+ G T H+ V+++
Sbjct: 195 HGISIGSIATGKHVSNVVIK 214
>pdb|4A25|A Chain A, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions.
pdb|4A25|B Chain B, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions.
pdb|4A25|C Chain C, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions.
pdb|4A25|D Chain D, X-ray Structure Dps From Kineococcus Radiotolerans In
Complex With Mn (ii) Ions
Length = 169
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 35 DPRPHSVSITEFGAVGDGKTLNTLAFQNAIFYLKSFADKGGAQLYVPSGKWLTGSFNLTS 94
D RP +V+ + G VG + ++T A AI L +++ P S +L
Sbjct: 88 DARPQTVAASRIGDVGPDE-IDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLH 146
Query: 95 HLTLFLEKGAVILGSQNPS 113
+TL LEK A ++GS+N S
Sbjct: 147 AITLELEKQAWMIGSENRS 165
>pdb|1IA5|A Chain A, Polygalacturonase From Aspergillus Aculeatus
pdb|1IB4|A Chain A, Crystal Structure Of Polygalacturonase From Aspergillus
Aculeatus At Ph4.5
pdb|1IB4|B Chain B, Crystal Structure Of Polygalacturonase From Aspergillus
Aculeatus At Ph4.5
Length = 339
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 145 RDVVVTGDNG-TIDGQGSVWWDWFSSQSLNYSRPHLVEFISSENVVVSNLTFLNAP 199
D+ +TG +G +I+G GS WWD ++P S N V+S L +N+P
Sbjct: 72 SDLTITGASGHSINGDGSRWWDGEGGNG-GKTKPKFFAAHSLTNSVISGLKIVNSP 126
>pdb|1HG8|A Chain A, Endopolygalacturonase From The Phytopathogenic Fungus
Fusarium Moniliforme
Length = 349
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 43/210 (20%), Positives = 79/210 (37%), Gaps = 28/210 (13%)
Query: 146 DVVVTGDNG-TIDGQGSVWWDWFSSQSLNYSRPH--LVEFISSENVVVSNLTFLNAPAYN 202
++ +TG +G IDG G +WD S S + +P +V ++ N ++NL N P +
Sbjct: 70 NITITGASGHVIDGNGQAYWDGKGSNSNSNQKPDHFIVVQKTTGNSKITNLNIQNWPVHC 129
Query: 203 IHPVYCSNVHIQ------------NISVHAPPESPYTVGIVPDSSDNVCIEDCIIAMGHD 250
S + I N + P + T G SSD+V +++ + D
Sbjct: 130 FDITGSSQLTISGLILDNRAGDKPNAKSGSLPAAHNTDGFDISSSDHVTLDNNHVYNQDD 189
Query: 251 AISLKSGWDEYGIAYGRPTTDVHIRRVLLQXXXXXXXXXXXXXXGGISN-VQVEKIHLYD 309
+++ SG T++ + + + + VQ + +
Sbjct: 190 CVAVTSG------------TNIVVSNMYCSGGHGLSIGSVGGKSDNVVDGVQFLSSQVVN 237
Query: 310 SLNGIEFRTTKGRGGYIRQIVISDAELYNI 339
S NG ++ G G I + + L NI
Sbjct: 238 SQNGCRIKSNSGATGTINNVTYQNIALTNI 267
>pdb|3GQ7|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene
Product 12 N- Terminal Fragment
pdb|3GQ8|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene
Product 12 N- Terminal Fragment In Complex With
2-(N-Cyclohexylamino)ethane Sulfonic Acid (Ches)
pdb|3GQ9|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene
Product 12 N- Terminal Fragment In An Apo Form
pdb|3GQA|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene
Product 12 N- Terminal Fragment In Complex With Cobalt
Ions
Length = 609
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 37 RPHSVSITEFGAVGDGKTLNTLAFQNAIFYLKSFADKGGAQLYVPSGKWL 86
+ VS+ +GA GDG T + AF+ AI + G +YVP G ++
Sbjct: 19 KQFGVSVKTYGAKGDGVTDDIRAFEKAI--------ESGFPVYVPYGTFM 60
>pdb|3SUC|A Chain A, Crystal Structure Of The Pre-Mature Bacteriophage Phi29
Gene Product 12
Length = 772
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 37 RPHSVSITEFGAVGDGKTLNTLAFQNAIFYLKSFADKGGAQLYVPSGKWL 86
+ VS+ +GA GDG T + AF+ AI + G +YVP G ++
Sbjct: 19 KQFGVSVKTYGAKGDGVTDDIRAFEKAI--------ESGFPVYVPYGTFM 60
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 0.138 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,305,369
Number of Sequences: 62578
Number of extensions: 547261
Number of successful extensions: 1049
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1035
Number of HSP's gapped (non-prelim): 15
length of query: 456
length of database: 14,973,337
effective HSP length: 102
effective length of query: 354
effective length of database: 8,590,381
effective search space: 3040994874
effective search space used: 3040994874
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: 53 (25.0 bits)