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= 040588
(252 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3B6I|A Chain A, Wrba From Escherichia Coli, Native Structure
pdb|3B6I|B Chain B, Wrba From Escherichia Coli, Native Structure
pdb|3B6J|A Chain A, Wrba From Escherichia Coli, Nadh Complex
pdb|3B6J|B Chain B, Wrba From Escherichia Coli, Nadh Complex
pdb|3B6K|A Chain A, Wrba From Escherichia Coli, Benzoquinone Complex
pdb|3B6K|B Chain B, Wrba From Escherichia Coli, Benzoquinone Complex
pdb|3B6M|A Chain A, Wrba From Escherichia Coli, Second Crystal Form
pdb|3B6M|B Chain B, Wrba From Escherichia Coli, Second Crystal Form
pdb|2R96|A Chain A, Crystal Structure Of E. Coli Wrba In Complex With Fmn
pdb|2R96|C Chain C, Crystal Structure Of E. Coli Wrba In Complex With Fmn
pdb|2R97|A Chain A, Crystal Structure Of E. Coli Wrba In Complex With Fmn
pdb|2R97|C Chain C, Crystal Structure Of E. Coli Wrba In Complex With Fmn
pdb|2RG1|A Chain A, Crystal Structure Of E. Coli Wrba Apoprotein
pdb|2RG1|B Chain B, Crystal Structure Of E. Coli Wrba Apoprotein
Length = 198
Score = 160 bits (405), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 84/199 (42%), Positives = 119/199 (59%), Gaps = 5/199 (2%)
Query: 48 KIFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVPQKGIEVPV 107
K+ +++YSMYGH+E +AR + +G +DG E V+ RVPET+P ++ E K K PV
Sbjct: 3 KVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFE--KAGGKTQTAPV 60
Query: 108 IAVDDLVHADGLLFGFPTRFGSMASQMKAFFDSTFHLWEQQRLAGVPAGFFVSXXXXXXX 167
+L D ++FG PTRFG+M+ QM+ F D T LW L G A F S
Sbjct: 61 ATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQ 120
Query: 168 XXXXAWTAITQLAHHGMVYVPIGYTFGTEMFGMDSLRGGSPYGAGVFS-GDGTRKPTETE 226
T T LAHHGMV VPIGY E+F + +RGG+PYGA + GDG+R+P++ E
Sbjct: 121 EQTITST-WTTLAHHGMVIVPIGYA-AQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEE 178
Query: 227 LALAEHQGKYMAAIVKKFS 245
L++A +QG+Y+A + K +
Sbjct: 179 LSIARYQGEYVAGLAVKLN 197
>pdb|2ZKI|A Chain A, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
pdb|2ZKI|B Chain B, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
pdb|2ZKI|C Chain C, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
pdb|2ZKI|D Chain D, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
pdb|2ZKI|E Chain E, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
pdb|2ZKI|F Chain F, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
pdb|2ZKI|G Chain G, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
pdb|2ZKI|H Chain H, Crystal Structure Of Hypothetical Trp Repressor Binding
Protein From Sul Folobus Tokodaii (St0872)
Length = 199
Score = 102 bits (255), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 71/201 (35%), Positives = 97/201 (48%), Gaps = 10/201 (4%)
Query: 49 IFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVP-QKGIEVPV 107
I ++FY YG + LA+ + KG + G E + RV ETLP E Q ++P K ++P
Sbjct: 7 ILVLFYG-YGSIVELAKEIGKGAEEA-GAEVKIRRVRETLPPEF--QSRIPFDKVKDIPE 62
Query: 108 IAVDDLVHADGLLFGFPTRFGSMASQMKAFFDSTFHLWEQQRLAGVPAGFFVSXXXXXXX 167
+ +DD+ ADG G PTR+G+MA +K F D+T LW+ L G P FF
Sbjct: 63 VTLDDMRWADGFAIGSPTRYGNMAGGLKTFLDTTAILWKDNVLYGKPVTFFTEASTVHGG 122
Query: 168 XXXXAWTAITQLAHHGMVYVPIGYTFGTEMFGMDSLRGGSPYGAGVFSGDGTRKPTETEL 227
T T H GM+ VPIGY E+F + GG PYGA + E E
Sbjct: 123 HETTILTMSTYAYHFGMIIVPIGYGI-PELF--QTTTGGGPYGATHLGSK--EELDEMER 177
Query: 228 ALAEHQGKYMAAIVKKFSHPN 248
+A QGK + + K N
Sbjct: 178 KIARFQGKRITEVAKAIKCCN 198
>pdb|1ZWK|A Chain A, Structure Of Wrba From Pseudomonas Aeruginosa
pdb|1ZWK|B Chain B, Structure Of Wrba From Pseudomonas Aeruginosa
pdb|1ZWL|A Chain A, Structure Of Wrba From Pseudomonas Aeruginosa In Complex
With Fmn
Length = 207
Score = 98.2 bits (243), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 66/197 (33%), Positives = 94/197 (47%), Gaps = 7/197 (3%)
Query: 49 IFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVPQKGIEVPVI 108
I +++YS +G +AR++ +GV+ G E + VP +P +G +
Sbjct: 15 ILVLYYSRHGATAEMARQIARGVEQ-GGFEARVRTVPAVSTECEAVAPDIPAEGALYATL 73
Query: 109 AVDDLVHADGLLFGFPTRFGSMASQMKAFFDSTFHLWEQQRLAGVPAGFFVSXXXXXXXX 168
+DL + GL G PTRFG+MAS +K F D T LW L G PA F S
Sbjct: 74 --EDLKNCAGLALGSPTRFGNMASPLKYFLDGTSSLWLTGSLVGKPAAVFTSTASLHGGQ 131
Query: 169 XXXAWTAITQLAHHGMVYVPIGYTFGTEMFGMDSLRGGSPYGAGVFSG-DGTRKPTETEL 227
+ + L HHGM+ + I Y +E +++ GG+PYGA F+G DG R E EL
Sbjct: 132 ETTQLSMLLPLLHHGMLVLGIPY---SEPALLETRGGGTPYGASHFAGADGKRSLDEHEL 188
Query: 228 ALAEHQGKYMAAIVKKF 244
L GK +A K
Sbjct: 189 TLCRALGKRLAETAGKL 205
>pdb|2A5L|A Chain A, The Crystal Structure Of The Trp Repressor Binding Protein
Wrba From Pseudomonas Aeruginosa
pdb|2A5L|B Chain B, The Crystal Structure Of The Trp Repressor Binding Protein
Wrba From Pseudomonas Aeruginosa
Length = 200
Score = 79.0 bits (193), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 64/197 (32%), Positives = 91/197 (46%), Gaps = 7/197 (3%)
Query: 49 IFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVPQKGIEVPVI 108
I +++YS +G AR++ +GV+ G E + VP +P +G +
Sbjct: 8 ILVLYYSRHGATAEXARQIARGVEQ-GGFEARVRTVPAVSTECEAVAPDIPAEGALYATL 66
Query: 109 AVDDLVHADGLLFGFPTRFGSMASQMKAFFDSTFHLWEQQRLAGVPAGFFVSXXXXXXXX 168
+DL + GL G PTRFG+ AS +K F D T LW L G PA F S
Sbjct: 67 --EDLKNCAGLALGSPTRFGNXASPLKYFLDGTSSLWLTGSLVGKPAAVFTSTASLHGGQ 124
Query: 169 XXXAWTAITQLAHHGMVYVPIGYTFGTEMFGMDSLRGGSPYGAGVFSG-DGTRKPTETEL 227
+ + L HHG + + I Y +E +++ GG+PYGA F+G DG R E EL
Sbjct: 125 ETTQLSXLLPLLHHGXLVLGIPY---SEPALLETRGGGTPYGASHFAGADGKRSLDEHEL 181
Query: 228 ALAEHQGKYMAAIVKKF 244
L GK +A K
Sbjct: 182 TLCRALGKRLAETAGKL 198
>pdb|1YDG|A Chain A, Crystal Structure Of Trp Repressor Binding Protein Wrba
pdb|1YDG|B Chain B, Crystal Structure Of Trp Repressor Binding Protein Wrba
pdb|1YDG|C Chain C, Crystal Structure Of Trp Repressor Binding Protein Wrba
pdb|1YDG|D Chain D, Crystal Structure Of Trp Repressor Binding Protein Wrba
pdb|1YDG|E Chain E, Crystal Structure Of Trp Repressor Binding Protein Wrba
pdb|1YDG|F Chain F, Crystal Structure Of Trp Repressor Binding Protein Wrba
pdb|1YDG|G Chain G, Crystal Structure Of Trp Repressor Binding Protein Wrba
pdb|1YDG|H Chain H, Crystal Structure Of Trp Repressor Binding Protein Wrba
Length = 211
Score = 63.9 bits (154), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 61/210 (29%), Positives = 88/210 (41%), Gaps = 18/210 (8%)
Query: 42 STTGQLKIFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVPQK 101
S T +K+ I+FYS G +A+ + + +L +V ET P +V++ +
Sbjct: 2 SLTAPVKLAIVFYSSTGTGYAMAQEAAEAGRAAGAEVRLL-KVRETAPQDVIDGQDAWKA 60
Query: 102 GIE----VPVIAVDDLVHADGLLFGFPTRFGSMASQMKAFFDSTFHLWEQQRLAGVPAGF 157
IE VP DL A+ ++F PTRFG SQM+AF D+ LW +LA
Sbjct: 61 NIEAMKDVPEATPADLEWAEAIVFSSPTRFGGATSQMRAFIDTLGGLWSSGKLANKTFSA 120
Query: 158 FVSXXXXXXXXXXXAWTAITQLAHHGMVYVPIGYTFGTEMFGMDSL---RGGSPYGAGVF 214
S T H G V P GYT D + GG+PYGA V
Sbjct: 121 MTSAQNVNGGQETTLQTLYMTAMHWGAVLTPPGYT--------DEVIFKSGGNPYGASV- 171
Query: 215 SGDGTRKPTETELALAEHQGKYMAAIVKKF 244
+ +G + E + A HQ + + K
Sbjct: 172 TANG-QPLLENDRASIRHQVRRQVELTAKL 200
>pdb|1YRH|A Chain A, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
pdb|1YRH|B Chain B, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
pdb|1YRH|C Chain C, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
pdb|1YRH|D Chain D, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
pdb|1YRH|E Chain E, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
pdb|1YRH|F Chain F, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
pdb|1YRH|G Chain G, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
pdb|1YRH|H Chain H, Crystal Structure Of Trp Repressor Binding Protein Wrba In
Complex With Fmn
Length = 211
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 60/210 (28%), Positives = 86/210 (40%), Gaps = 18/210 (8%)
Query: 42 STTGQLKIFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVPQK 101
S T +K+ I+FYS G A+ + + +L +V ET P +V++ +
Sbjct: 2 SLTAPVKLAIVFYSSTGTGYAXAQEAAEAGRAAGAEVRLL-KVRETAPQDVIDGQDAWKA 60
Query: 102 GIE----VPVIAVDDLVHADGLLFGFPTRFGSMASQMKAFFDSTFHLWEQQRLAGVPAGF 157
IE VP DL A+ ++F PTRFG SQ +AF D+ LW +LA
Sbjct: 61 NIEAXKDVPEATPADLEWAEAIVFSSPTRFGGATSQXRAFIDTLGGLWSSGKLANKTFSA 120
Query: 158 FVSXXXXXXXXXXXAWTAITQLAHHGMVYVPIGYTFGTEMFGMDSL---RGGSPYGAGVF 214
S T H G V P GYT D + GG+PYGA V
Sbjct: 121 XTSAQNVNGGQETTLQTLYXTAXHWGAVLTPPGYT--------DEVIFKSGGNPYGASV- 171
Query: 215 SGDGTRKPTETELALAEHQGKYMAAIVKKF 244
+ +G + E + A HQ + + K
Sbjct: 172 TANG-QPLLENDRASIRHQVRRQVELTAKL 200
>pdb|2ARK|A Chain A, Structure Of A Flavodoxin From Aquifex Aeolicus
pdb|2ARK|B Chain B, Structure Of A Flavodoxin From Aquifex Aeolicus
pdb|2ARK|C Chain C, Structure Of A Flavodoxin From Aquifex Aeolicus
pdb|2ARK|D Chain D, Structure Of A Flavodoxin From Aquifex Aeolicus
pdb|2ARK|E Chain E, Structure Of A Flavodoxin From Aquifex Aeolicus
pdb|2ARK|F Chain F, Structure Of A Flavodoxin From Aquifex Aeolicus
Length = 188
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 42/99 (42%), Gaps = 22/99 (22%)
Query: 48 KIFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVPQKGIEVPV 107
K+ +I+ + G+ + A + +G S++G E L V E
Sbjct: 6 KVLVIYDTRTGNTKKXAELVAEGARSLEGTEVRLKHVDEATK------------------ 47
Query: 108 IAVDDLVHADGLLFGFPTRFGSMASQMKAFFDSTF-HLW 145
+D++ ADGL G PT G ++ + K FFD LW
Sbjct: 48 ---EDVLWADGLAVGSPTNXGLVSWKXKRFFDDVLGDLW 83
>pdb|2DQB|A Chain A, Crystal Structure Of Dntp Triphosphohydrolase From Thermus
Thermophilus Hb8, Which Is Homologous To Dgtp
Triphosphohydrolase
pdb|2DQB|B Chain B, Crystal Structure Of Dntp Triphosphohydrolase From Thermus
Thermophilus Hb8, Which Is Homologous To Dgtp
Triphosphohydrolase
pdb|2DQB|C Chain C, Crystal Structure Of Dntp Triphosphohydrolase From Thermus
Thermophilus Hb8, Which Is Homologous To Dgtp
Triphosphohydrolase
pdb|2DQB|D Chain D, Crystal Structure Of Dntp Triphosphohydrolase From Thermus
Thermophilus Hb8, Which Is Homologous To Dgtp
Triphosphohydrolase
pdb|2DQB|E Chain E, Crystal Structure Of Dntp Triphosphohydrolase From Thermus
Thermophilus Hb8, Which Is Homologous To Dgtp
Triphosphohydrolase
pdb|2DQB|F Chain F, Crystal Structure Of Dntp Triphosphohydrolase From Thermus
Thermophilus Hb8, Which Is Homologous To Dgtp
Triphosphohydrolase
Length = 376
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 47 LKIFIIFYSMYGHVEILARRMKKGVDSIDGVEGVLYRVPETLPAEVLEQMKVPQKGIEVP 106
LK F+ Y H E+L R +K ++G+ R PE LP EV Q K+P++G+E
Sbjct: 299 LKAFLX-ERFYRHPEVL-RERRKAEAVLEGLFAAYTRYPELLPREV--QAKIPEEGLERA 354
Query: 107 VI 108
V
Sbjct: 355 VC 356
>pdb|3Q7U|A Chain A, Structure Of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd) Complexed With Ctp
pdb|3Q7U|B Chain B, Structure Of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd) Complexed With Ctp
pdb|3Q80|A Chain A, Structure Of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd) Complexed With Cdp-Me
pdb|3Q80|B Chain B, Structure Of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd) Complexed With Cdp-Me
Length = 231
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 85 PETLPAEVLEQMKVPQKGIEVPVIAVDDL---VHADGLLFGFPTRFGSMASQMKAFFDST 141
P L A V+E ++ + VPV+ + D V A+G++ G P R G A Q F +
Sbjct: 114 PPALVARVVEALRDGYAAV-VPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTD 172
Query: 142 FHLWEQQR 149
L QR
Sbjct: 173 LLLRSYQR 180
>pdb|3OKR|A Chain A, Structure Of Mtb Apo 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd)
pdb|3OKR|B Chain B, Structure Of Mtb Apo 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd)
pdb|3OKR|C Chain C, Structure Of Mtb Apo 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd)
pdb|3OKR|D Chain D, Structure Of Mtb Apo 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidyltransferase (Ispd)
Length = 231
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 85 PETLPAEVLEQMKVPQKGIEVPVIAVDDL---VHADGLLFGFPTRFGSMASQMKAFFDST 141
P L A V+E ++ + VPV+ + D V A+G++ G P R G A Q F +
Sbjct: 114 PPALVARVVEALRDGYAAV-VPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTD 172
Query: 142 FHLWEQQR 149
L QR
Sbjct: 173 LLLRSYQR 180
>pdb|2XWN|A Chain A, Crystal Structure Of Ispd From Mycobacterium Tuberculosis
In Complex With Ctp And Mg
pdb|2XWN|B Chain B, Crystal Structure Of Ispd From Mycobacterium Tuberculosis
In Complex With Ctp And Mg
Length = 233
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 85 PETLPAEVLEQMKVPQKGIEVPVIAVDDL---VHADGLLFGFPTRFGSMASQMKAFFDST 141
P L A V+E ++ + VPV+ + D V A+G++ G P R G A Q F +
Sbjct: 114 PPALVARVVEALRDGYAAV-VPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTD 172
Query: 142 FHLWEQQR 149
L QR
Sbjct: 173 LLLRSYQR 180
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 0.137 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,898,033
Number of Sequences: 62578
Number of extensions: 324680
Number of successful extensions: 723
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 706
Number of HSP's gapped (non-prelim): 14
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
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: 50 (23.9 bits)