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= psy10850
(173 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JGB|A Chain A, Structure Of Human Eif4e Homologous Protein 4ehp With
M7gtp
pdb|2JGC|A Chain A, Structure Of The Human Eif4e Homologous Protein, 4ehp
Without Ligand Bound
Length = 195
Score = 226 bits (576), Expect = 6e-60, Method: Compositional matrix adjust.
Identities = 100/138 (72%), Positives = 115/138 (83%)
Query: 32 PHHHKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSF 91
P H LQY Y FWYSRRTPG+ TS QSY+ N+K I F SVEQFW Y+H+VRP +
Sbjct: 12 PAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGH 71
Query: 92 IDLHLFKVGVKPMWEDEANRNGGKWLIRLRKGIASRCWENLILAMLGEQFMVGDEICGAV 151
D HLFK G+KPMWED+AN+NGGKW+IRLRKG+ASRCWENLILAMLGEQFMVG+EICGAV
Sbjct: 72 SDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLILAMLGEQFMVGEEICGAV 131
Query: 152 ISVRFQEDHISVWNKTSS 169
+SVRFQED IS+WNKT+S
Sbjct: 132 VSVRFQEDIISIWNKTAS 149
>pdb|2WMC|A Chain A, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
pdb|2WMC|B Chain B, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
pdb|2WMC|C Chain C, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
pdb|2WMC|D Chain D, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
pdb|2WMC|E Chain E, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
pdb|2WMC|F Chain F, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
pdb|2WMC|G Chain G, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
pdb|2WMC|H Chain H, Crystal Structure Of Eukaryotic Initiation Factor 4e From
Pisum Sativum
Length = 178
Score = 109 bits (272), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 52/135 (38%), Positives = 78/135 (57%), Gaps = 2/135 (1%)
Query: 35 HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDL 94
H L+ + FW+ TP + ++ +++ I F +VE+FW IY ++ P + D
Sbjct: 3 HLLENSWTFWFD--TPAAKSKQAAWGSSMRPIYTFSTVEEFWSIYNNIHHPGKLAVGADF 60
Query: 95 HLFKVGVKPMWEDEANRNGGKWLIRLRKGIASRCWENLILAMLGEQFMVGDEICGAVISV 154
+ FK ++P WED NGGKW KG + W +LAM+GEQF GDEICGAV++V
Sbjct: 61 YCFKHKIEPKWEDPICANGGKWTANYPKGKSDTSWLYTLLAMIGEQFDHGDEICGAVVNV 120
Query: 155 RFQEDHISVWNKTSS 169
R + + IS+W K +S
Sbjct: 121 RGRAEKISIWTKNAS 135
>pdb|2IDV|A Chain A, Crystal Structure Of Wheat C113s Mutant Eif4e Bound To 7-
Methyl-Gdp
Length = 177
Score = 108 bits (269), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 49/135 (36%), Positives = 79/135 (58%), Gaps = 2/135 (1%)
Query: 35 HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDL 94
H L+ + FW+ P + ++ + I F +VE FW +Y ++ P++ D
Sbjct: 2 HPLENAWTFWFD--NPQGKSRQVAWGSTIHPIHTFSTVEDFWGLYNNIHNPSKLNVGADF 59
Query: 95 HLFKVGVKPMWEDEANRNGGKWLIRLRKGIASRCWENLILAMLGEQFMVGDEICGAVISV 154
H FK ++P WED + NGGKW I +G + W + +LAM+GEQF GDEICGAV+SV
Sbjct: 60 HCFKNKIEPKWEDPISANGGKWTISCGRGKSDTFWLHTLLAMIGEQFDFGDEICGAVVSV 119
Query: 155 RFQEDHISVWNKTSS 169
R +++ +++W K ++
Sbjct: 120 RQKQERVAIWTKNAA 134
>pdb|2IDR|A Chain A, Crystal Structure Of Translation Initiation Factor Eif4e
From Wheat
pdb|2IDR|B Chain B, Crystal Structure Of Translation Initiation Factor Eif4e
From Wheat
Length = 177
Score = 107 bits (267), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 49/135 (36%), Positives = 78/135 (57%), Gaps = 2/135 (1%)
Query: 35 HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDL 94
H L+ + FW+ P + ++ + I F +VE FW +Y ++ P++ D
Sbjct: 2 HPLENAWTFWFD--NPQGKSRQVAWGSTIHPIHTFSTVEDFWGLYNNIHNPSKLNVGADF 59
Query: 95 HLFKVGVKPMWEDEANRNGGKWLIRLRKGIASRCWENLILAMLGEQFMVGDEICGAVISV 154
H FK ++P WED NGGKW I +G + W + +LAM+GEQF GDEICGAV+SV
Sbjct: 60 HCFKNKIEPKWEDPICANGGKWTISCGRGKSDTFWLHTLLAMIGEQFDFGDEICGAVVSV 119
Query: 155 RFQEDHISVWNKTSS 169
R +++ +++W K ++
Sbjct: 120 RQKQERVAIWTKNAA 134
>pdb|2W97|B Chain B, Crystal Structure Of Eif4e Bound To Glycerol And Eif4g1
Peptide
Length = 217
Score = 106 bits (264), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 54/141 (38%), Positives = 82/141 (58%), Gaps = 12/141 (8%)
Query: 31 PPHH--HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEF 88
P H+ H LQ ++ W+ ++ K ++ NL+LI KF +VE FW +Y H+ +
Sbjct: 31 PEHYIKHPLQNRWALWFFKKDKSK-----TWQANLRLISKFDTVEDFWALYNHIQLSSNL 85
Query: 89 QSFIDLHLFKVGVKPMWEDEANRNGGKWLIRL----RKGIASRCWENLILAMLGEQF-MV 143
D LFK G++PMWEDE N+ GG+WLI L R+ R W +L ++GE F
Sbjct: 86 MPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY 145
Query: 144 GDEICGAVISVRFQEDHISVW 164
D++CGAV++VR + D I++W
Sbjct: 146 SDDVCGAVVNVRAKGDKIAIW 166
>pdb|1IPB|A Chain A, Crystal Structure Of Eukaryotic Initiation Factor 4e
Complexed With 7-methyl Gpppa
pdb|1IPC|A Chain A, Crystal Structure Of Eukaryotic Initiation Factor 4e
Complexed With 7-methyl Gtp
pdb|2GPQ|A Chain A, Cap-Free Structure Of Eif4e Suggests Basis For Its
Allosteric Regulation
pdb|2V8W|A Chain A, Crystallographic And Mass Spectrometric Characterisation
Of Eif4e With N7-Cap Derivatives
pdb|2V8W|E Chain E, Crystallographic And Mass Spectrometric Characterisation
Of Eif4e With N7-Cap Derivatives
pdb|2V8X|A Chain A, Crystallographic And Mass Spectrometric Characterisation
Of Eif4e With N7-Cap Derivatives
pdb|2V8X|E Chain E, Crystallographic And Mass Spectrometric Characterisation
Of Eif4e With N7-Cap Derivatives
pdb|2V8Y|A Chain A, Crystallographic And Mass Spectrometric Characterisation
Of Eif4e With N7-Cap Derivatives
pdb|2V8Y|E Chain E, Crystallographic And Mass Spectrometric Characterisation
Of Eif4e With N7-Cap Derivatives
pdb|2W97|A Chain A, Crystal Structure Of Eif4e Bound To Glycerol And Eif4g1
Peptide
pdb|3TF2|A Chain A, Crystal Structure Of The Cap Free Human Translation
Initiation Factor Eif4e
pdb|3TF2|B Chain B, Crystal Structure Of The Cap Free Human Translation
Initiation Factor Eif4e
pdb|3TF2|C Chain C, Crystal Structure Of The Cap Free Human Translation
Initiation Factor Eif4e
pdb|3TF2|D Chain D, Crystal Structure Of The Cap Free Human Translation
Initiation Factor Eif4e
pdb|3U7X|A Chain A, Crystal Structure Of The Human Eif4e-4ebp1 Peptide Complex
Without Cap
pdb|3U7X|B Chain B, Crystal Structure Of The Human Eif4e-4ebp1 Peptide Complex
Without Cap
pdb|4AZA|A Chain A, Improved Eif4e Binding Peptides By Phage Display Guided
Design.
pdb|4AZA|C Chain C, Improved Eif4e Binding Peptides By Phage Display Guided
Design
Length = 217
Score = 105 bits (261), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 54/141 (38%), Positives = 81/141 (57%), Gaps = 12/141 (8%)
Query: 31 PPHH--HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEF 88
P H+ H LQ ++ W+ + K ++ NL+LI KF +VE FW +Y H+ +
Sbjct: 31 PEHYIKHPLQNRWALWFFKNDKSK-----TWQANLRLISKFDTVEDFWALYNHIQLSSNL 85
Query: 89 QSFIDLHLFKVGVKPMWEDEANRNGGKWLIRL----RKGIASRCWENLILAMLGEQF-MV 143
D LFK G++PMWEDE N+ GG+WLI L R+ R W +L ++GE F
Sbjct: 86 MPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY 145
Query: 144 GDEICGAVISVRFQEDHISVW 164
D++CGAV++VR + D I++W
Sbjct: 146 SDDVCGAVVNVRAKGDKIAIW 166
>pdb|4DT6|A Chain A, Co-Crystal Structure Of Eif4e With Inhibitor
pdb|4DUM|A Chain A, Co-Crystal Structure Of Eif4e With Inhibitor
Length = 240
Score = 105 bits (261), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 54/141 (38%), Positives = 81/141 (57%), Gaps = 12/141 (8%)
Query: 31 PPHH--HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEF 88
P H+ H LQ ++ W+ + K ++ NL+LI KF +VE FW +Y H+ +
Sbjct: 54 PEHYIKHPLQNRWALWFFKNDKSK-----TWQANLRLISKFDTVEDFWALYNHIQLSSNL 108
Query: 89 QSFIDLHLFKVGVKPMWEDEANRNGGKWLIRL----RKGIASRCWENLILAMLGEQF-MV 143
D LFK G++PMWEDE N+ GG+WLI L R+ R W +L ++GE F
Sbjct: 109 MPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY 168
Query: 144 GDEICGAVISVRFQEDHISVW 164
D++CGAV++VR + D I++W
Sbjct: 169 SDDVCGAVVNVRAKGDKIAIW 189
>pdb|1EJ1|A Chain A, Cocrystal Structure Of The Messenger Rna 5' Cap-Binding
Protein (Eif4e) Bound To 7-Methyl-Gdp
pdb|1EJ1|B Chain B, Cocrystal Structure Of The Messenger Rna 5' Cap-Binding
Protein (Eif4e) Bound To 7-Methyl-Gdp
pdb|1EJ4|A Chain A, Cocrystal Structure Of Eif4e4E-Bp1 Peptide
pdb|1EJH|A Chain A, Eif4eEIF4G PEPTIDE7-Methyl-Gdp
pdb|1EJH|B Chain B, Eif4eEIF4G PEPTIDE7-Methyl-Gdp
pdb|1EJH|C Chain C, Eif4eEIF4G PEPTIDE7-Methyl-Gdp
pdb|1EJH|D Chain D, Eif4eEIF4G PEPTIDE7-Methyl-Gdp
pdb|1L8B|A Chain A, Cocrystal Structure Of The Messenger Rna 5' Cap-Binding
Protein (Eif4e) Bound To 7-Methylgpppg
pdb|1L8B|B Chain B, Cocrystal Structure Of The Messenger Rna 5' Cap-Binding
Protein (Eif4e) Bound To 7-Methylgpppg
Length = 190
Score = 104 bits (260), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 54/141 (38%), Positives = 81/141 (57%), Gaps = 12/141 (8%)
Query: 31 PPHH--HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEF 88
P H+ H LQ ++ W+ + K ++ NL+LI KF +VE FW +Y H+ +
Sbjct: 4 PEHYIKHPLQNRWALWFFKNDKSK-----TWQANLRLISKFDTVEDFWALYNHIQLSSNL 58
Query: 89 QSFIDLHLFKVGVKPMWEDEANRNGGKWLIRL----RKGIASRCWENLILAMLGEQF-MV 143
D LFK G++PMWEDE N+ GG+WLI L R+ R W +L ++GE F
Sbjct: 59 MPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY 118
Query: 144 GDEICGAVISVRFQEDHISVW 164
D++CGAV++VR + D I++W
Sbjct: 119 SDDVCGAVVNVRAKGDKIAIW 139
>pdb|1WKW|A Chain A, Crystal Structure Of The Ternary Complex Of Eif4e-M7gpppa-
4ebp1 Peptide
pdb|3AM7|A Chain A, Crystal Structure Of The Ternary Complex Of
Eif4e-M7gtp-4ebp2 Peptide
Length = 191
Score = 104 bits (260), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 54/141 (38%), Positives = 81/141 (57%), Gaps = 12/141 (8%)
Query: 31 PPHH--HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEF 88
P H+ H LQ ++ W+ + K ++ NL+LI KF +VE FW +Y H+ +
Sbjct: 5 PEHYIKHPLQNRWALWFFKNDKSK-----TWQANLRLISKFDTVEDFWALYNHIQLSSNL 59
Query: 89 QSFIDLHLFKVGVKPMWEDEANRNGGKWLIRL----RKGIASRCWENLILAMLGEQF-MV 143
D LFK G++PMWEDE N+ GG+WLI L R+ R W +L ++GE F
Sbjct: 60 MPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY 119
Query: 144 GDEICGAVISVRFQEDHISVW 164
D++CGAV++VR + D I++W
Sbjct: 120 SDDVCGAVVNVRAKGDKIAIW 140
>pdb|4AXG|A Chain A, Structure Of Eif4e-Cup Complex
pdb|4AXG|B Chain B, Structure Of Eif4e-Cup Complex
Length = 248
Score = 102 bits (253), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 50/135 (37%), Positives = 76/135 (56%), Gaps = 8/135 (5%)
Query: 33 HHHKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFI 92
+ H L + WY K S++D I F +VE FW +Y H+ P+E +
Sbjct: 68 YKHPLMNVWTLWYLENDRSK-----SWEDMQNEITSFDTVEDFWSLYNHIKPPSEIKLGS 122
Query: 93 DLHLFKVGVKPMWEDEANRNGGKWLIRLRKGIAS---RCWENLILAMLGEQFMVGDEICG 149
D LFK ++PMWED AN+ GG+W+I L K + W +++L ++GE F D+ICG
Sbjct: 123 DYSLFKKNIRPMWEDAANKQGGRWVITLNKSSKTDLDNLWLDVLLCLIGEAFDHSDQICG 182
Query: 150 AVISVRFQEDHISVW 164
AVI++R + + IS+W
Sbjct: 183 AVINIRGKSNKISIW 197
>pdb|3M93|A Chain A, Complex Crystal Structure Of Ascaris Suum Eif4e-3 With M7g
Cap
pdb|3M94|A Chain A, Complex Crystal Structure Of Ascaris Suum Eif4e-3 With
M2,2,7g Cap
Length = 189
Score = 99.0 bits (245), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 53/139 (38%), Positives = 79/139 (56%), Gaps = 10/139 (7%)
Query: 35 HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDL 94
H LQ + WY K + ++D LK + F +VE FW +Y H+ + D
Sbjct: 3 HPLQCHWALWYL-----KADRSKDWEDCLKQVAVFDTVEDFWSLYNHIQAASGLTWGSDY 57
Query: 95 HLFKVGVKPMWEDEANRNGGKWLI----RLRKGIASRCWENLILAMLGEQFM-VGDEICG 149
+LFK G+KPMWEDE N GG+WL+ + R + W L++A++GEQF G+ ICG
Sbjct: 58 YLFKEGIKPMWEDENNVKGGRWLVVVDKQKRAQLLDHYWLELLMAIIGEQFEDNGEYICG 117
Query: 150 AVISVRFQEDHISVWNKTS 168
AV++VR + D +S+W + S
Sbjct: 118 AVVNVRQKGDKVSLWTRDS 136
>pdb|4B6V|A Chain A, The Third Member Of The Eif4e Family Represses Gene
Expression Via A Novel Mode Of Recognition Of The
Methyl-7 Guanosine Cap Moiety
Length = 207
Score = 89.7 bits (221), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 53/155 (34%), Positives = 76/155 (49%), Gaps = 8/155 (5%)
Query: 20 DISLEDLPLTIPPHHHKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIY 79
D +L LP P L + FW R PG + NLK I +V+ FW +Y
Sbjct: 17 DKALSALPPE--PGGVPLHSPWTFWLDRSLPG--ATAAECASNLKKIYTVQTVQIFWSVY 72
Query: 80 THLVRPNEFQSFIDLHLFKVGVKPMWEDEANRNGGKWLIRLRKGIASRCWENLILAMLGE 139
++ HL + +P+WE+E+N GG W +++ K S W+ L+LA +GE
Sbjct: 73 NNIPPVTSLPLRCSYHLMRGERRPLWEEESNAKGGVWKMKVPKDSTSTVWKELLLATIGE 132
Query: 140 QFM----VGDEICGAVISVRFQEDHISVWNKTSSL 170
QF DEI G +SVR +ED + VWN +SL
Sbjct: 133 QFTDCAAADDEIIGVSVSVRDREDVVQVWNVNASL 167
>pdb|3HXG|A Chain A, Crystal Structure Of Schistsome Eif4e Complexed With
M7gpppa And 4e-Bp
pdb|3HXI|A Chain A, Crystal Structure Of Schistosome Eif4e Complexed With
M7gpppg And 4e-Bp
Length = 189
Score = 86.3 bits (212), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 48/144 (33%), Positives = 74/144 (51%), Gaps = 13/144 (9%)
Query: 27 PLTIPPHHHKLQ--YQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVR 84
PL P H LQ + Y+ + R+ +D+ L+ + F ++E FW + TH VR
Sbjct: 2 PLGSPEFPHPLQDSWSYYLFQFRK-------ALDWDECLEKVATFSTIEDFWSVLTHTVR 54
Query: 85 PNEFQSFIDLHLFKVGVKPMWEDEANRNGGKWLIRLR-KGIASRCWENLILAMLGEQFMV 143
P E DL++FK + P WED N NGG+WLI + + W+ L++ ++G +
Sbjct: 55 PREITYGKDLYMFKSDIMPKWEDPKNENGGRWLINVTARQDVDFLWDELLMLLIGSDWDT 114
Query: 144 GDE---ICGAVISVRFQEDHISVW 164
+E ICGAV R + +SVW
Sbjct: 115 DEEDRQICGAVFQPRSRGSKLSVW 138
>pdb|1AP8|A Chain A, Translation Initiation Factor Eif4e In Complex With M7gdp,
Nmr, 20 Structures
Length = 213
Score = 86.3 bits (212), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 47/136 (34%), Positives = 74/136 (54%), Gaps = 6/136 (4%)
Query: 35 HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDL 94
H L ++ WY++ V +S+ D L+ + F +VE+FW I ++ P+E D
Sbjct: 37 HPLNTKWTLWYTKPA---VDKSESWSDLLRPVTSFQTVEEFWAIIQNIPEPHELPLKSDY 93
Query: 95 HLFKVGVKPMWEDEANRNGGKWLIRLRKGIA--SRCWENLILAMLGEQFMVGD-EICGAV 151
H+F+ V+P WEDEAN GGKW +LR A W +LA++GE D +I G V
Sbjct: 94 HVFRNDVRPEWEDEANAKGGKWSFQLRGKGADIDELWLRTLLAVIGETIDEDDSQINGVV 153
Query: 152 ISVRFQEDHISVWNKT 167
+S+R + ++W K+
Sbjct: 154 LSIRKGGNKFALWTKS 169
>pdb|1RF8|A Chain A, Solution Structure Of The Yeast Translation Initiation
Factor Eif4e In Complex With M7gdp And Eif4gi Residues
393 To 490
Length = 213
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 45/135 (33%), Positives = 72/135 (53%), Gaps = 6/135 (4%)
Query: 35 HKLQYQYWFWYSRRTPGKVTSVQSYDDNLKLIQKFGSVEQFWEIYTHLVRPNEFQSFIDL 94
H L ++ WY++ V +S+ D L+ + F +VE+FW I ++ P+E D
Sbjct: 37 HPLNTKWTLWYTKPA---VDKSESWSDLLRPVTSFQTVEEFWAIIQNIPEPHELPLKSDY 93
Query: 95 HLFKVGVKPMWEDEANRNGGKWLIRL--RKGIASRCWENLILAMLGEQFMVGD-EICGAV 151
H+F+ V+P WEDEAN GGKW +L + W +LA++GE D +I G V
Sbjct: 94 HVFRNDVRPEWEDEANAKGGKWSFQLCGKGADIDELWLCTLLAVIGETIDEDDSQINGVV 153
Query: 152 ISVRFQEDHISVWNK 166
+S+R + ++W K
Sbjct: 154 LSIRKGGNKFALWTK 168
>pdb|1OS5|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase Complexed
With A Novel Non-Competitive Inhibitor
Length = 576
Score = 28.1 bits (61), Expect = 2.8, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K +Y Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGY 103
>pdb|3FRZ|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase In Complex
With
Length = 576
Score = 28.1 bits (61), Expect = 2.8, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K +Y Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGY 103
>pdb|2HAI|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase In Complex
With Novel Class Of Dihydropyrone-Containing Inhibitor
Length = 576
Score = 28.1 bits (61), Expect = 2.8, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K +Y Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGY 103
>pdb|1NB4|A Chain A, Hc-J4 Rna Polymerase Apo-Form
pdb|1NB4|B Chain B, Hc-J4 Rna Polymerase Apo-Form
pdb|1NB6|A Chain A, Hc-J4 Rna Polymerase Complexed With Utp
pdb|1NB6|B Chain B, Hc-J4 Rna Polymerase Complexed With Utp
pdb|1NB7|A Chain A, Hc-J4 Rna Polymerase Complexed With Short Rna Template
Strand
pdb|1NB7|B Chain B, Hc-J4 Rna Polymerase Complexed With Short Rna Template
Strand
Length = 570
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 103
>pdb|4DRU|A Chain A, Hcv Ns5b In Complex With Macrocyclic Indole Inhibitor
pdb|4DRU|B Chain B, Hcv Ns5b In Complex With Macrocyclic Indole Inhibitor
Length = 563
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 103
>pdb|3UPI|A Chain A, Synthesis Of Novel 4,5-Dihydrofurano Indoles And Their
Evaluation As Hcv Ns5b Polymerase Inhibitors
pdb|3UPI|B Chain B, Synthesis Of Novel 4,5-Dihydrofurano Indoles And Their
Evaluation As Hcv Ns5b Polymerase Inhibitors
Length = 585
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 103
>pdb|3U4O|A Chain A, Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of Indole
C2 Acyl Sulfonamides
pdb|3U4O|B Chain B, Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of Indole
C2 Acyl Sulfonamides
pdb|3U4R|A Chain A, Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of Indole
C2 Acyl Sulfonamides
pdb|3U4R|B Chain B, Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of Indole
C2 Acyl Sulfonamides
Length = 578
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 103
>pdb|2XHV|A Chain A, Hcv-J4 Ns5b Polymerase Point Mutant Orthorhombic Crystal
Form
pdb|2XHV|B Chain B, Hcv-J4 Ns5b Polymerase Point Mutant Orthorhombic Crystal
Form
Length = 579
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 68 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 104
>pdb|2XHU|A Chain A, Hcv-J4 Ns5b Polymerase Orthorhombic Crystal Form
pdb|2XHU|B Chain B, Hcv-J4 Ns5b Polymerase Orthorhombic Crystal Form
pdb|2XHW|A Chain A, Hcv-J4 Ns5b Polymerase Trigonal Crystal Form
Length = 579
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 68 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 104
>pdb|3MWV|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase
pdb|3MWV|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase
pdb|3MWW|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase
pdb|3MWW|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase
pdb|4GMC|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase In Complex With A
Thumb Inhibitor
pdb|4GMC|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase In Complex With A
Thumb Inhibitor
Length = 576
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 103
>pdb|3LKH|A Chain A, Inhibitors Of Hepatitis C Virus Polymerase: Synthesis And
Characterization Of Novel
6-Fluoro-N-[2-Hydroxy-1(S)-Benzam
pdb|3LKH|B Chain B, Inhibitors Of Hepatitis C Virus Polymerase: Synthesis And
Characterization Of Novel
6-Fluoro-N-[2-Hydroxy-1(S)-Benzam
pdb|3SKA|A Chain A, I. Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of
Indole 2- Carboxylic Acids With C3-Heterocycles
pdb|3SKA|B Chain B, I. Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of
Indole 2- Carboxylic Acids With C3-Heterocycles
pdb|3SKE|A Chain A, I. Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of
Indole 2- Carboxylic Acids With C3-Heterocycles
pdb|3SKE|B Chain B, I. Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of
Indole 2- Carboxylic Acids With C3-Heterocycles
pdb|3SKH|A Chain A, I. Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of
Indole 2- Carboxylic Acids With C3-Heterocycles
pdb|3SKH|B Chain B, I. Novel Hcv Ns5b Polymerase Inhibitors: Discovery Of
Indole 2- Carboxylic Acids With C3-Heterocycles
pdb|3UPH|A Chain A, Synthesis Of Novel 4,5-Dihydrofurano Indoles And Their
Evaluation As Hcv Ns5b Polymerase Inhibitors
pdb|3UPH|B Chain B, Synthesis Of Novel 4,5-Dihydrofurano Indoles And Their
Evaluation As Hcv Ns5b Polymerase Inhibitors
pdb|3TYQ|A Chain A, Sar Development And Discovery Of Potent Indole-Based
Inhibitors Of The Hepatitis C Virus Ns5b Polymerase
pdb|3TYQ|B Chain B, Sar Development And Discovery Of Potent Indole-Based
Inhibitors Of The Hepatitis C Virus Ns5b Polymerase
pdb|3TYV|A Chain A, Sar Development And Discovery Of Potent Indole-Based
Inhibitors Of The Hepatitis C Virus Ns5b Polymerase
pdb|3TYV|B Chain B, Sar Development And Discovery Of Potent Indole-Based
Inhibitors Of The Hepatitis C Virus Ns5b Polymerase
Length = 576
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 103
>pdb|3CSO|A Chain A, Hcv Polymerase In Complex With A 1,5 Benzodiazepine
Inhibitor
pdb|3CSO|B Chain B, Hcv Polymerase In Complex With A 1,5 Benzodiazepine
Inhibitor
pdb|3GOL|A Chain A, Hcv Ns5b Polymerase In Complex With 1,5 Benzodiazepine
Inhibitor (R)- 11d
pdb|3GOL|B Chain B, Hcv Ns5b Polymerase In Complex With 1,5 Benzodiazepine
Inhibitor (R)- 11d
pdb|3GNV|A Chain A, Hcv Ns5b Polymerase In Complex With 1,5 Benzodiazepine
Inhibitor 1b
pdb|3GNV|B Chain B, Hcv Ns5b Polymerase In Complex With 1,5 Benzodiazepine
Inhibitor 1b
pdb|3GNW|A Chain A, Hcv Ns5b Polymerase In Complex With 1,5 Benzodiazepine
Inhibitor 4c
pdb|3GNW|B Chain B, Hcv Ns5b Polymerase In Complex With 1,5 Benzodiazepine
Inhibitor 4c
pdb|3HKY|A Chain A, Hcv Ns5b Polymerase Genotype 1b In Complex With 1,5
Benzodiazepine 6
pdb|3HKY|B Chain B, Hcv Ns5b Polymerase Genotype 1b In Complex With 1,5
Benzodiazepine 6
Length = 581
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 70 VLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGY 106
>pdb|3QGH|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Genotype 1a Complex With
N-Cyclopropyl-6-[(3r)-3-{[4-
(Trifluoromethoxy)benzyl]carbamoyl}-4-{[4-
(Trifluoromethoxy)
Phenyl]sulfonyl}piperazin-1-Yl]pyridazine-3-Carboxamide
pdb|3QGI|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Genotype 1a Complex With
N-[(2s)-Butan-2-Yl]-6-[(3r)-3-
{[4-(Trifluoromethoxy)benzyl]carbamoyl}-4-{[4-
(Trifluoromethoxy)
Phenyl]sulfonyl}piperazin-1-Yl]pyridazine-3-Carboxamide
Length = 571
Score = 26.6 bits (57), Expect = 7.8, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK V+ S +K + +S+E+ PPH K ++ Y
Sbjct: 68 VLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKFGY 104
>pdb|2XI2|A Chain A, Hcv-H77 Ns5b Apo Polymerase
pdb|2XI2|B Chain B, Hcv-H77 Ns5b Apo Polymerase
pdb|2XI2|C Chain C, Hcv-H77 Ns5b Apo Polymerase
pdb|2XI3|A Chain A, Hcv-H77 Ns5b Polymerase Complexed With Gtp
pdb|2XI3|B Chain B, Hcv-H77 Ns5b Polymerase Complexed With Gtp
Length = 576
Score = 26.6 bits (57), Expect = 7.8, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK V+ S +K + +S+E+ PPH K ++ Y
Sbjct: 67 VLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKFGY 103
>pdb|2AWZ|A Chain A, Hepatitis C Virus Ns5b Rna Polymerase In Complex With A
Covalent Inhibitor (5h)
pdb|2AWZ|B Chain B, Hepatitis C Virus Ns5b Rna Polymerase In Complex With A
Covalent Inhibitor (5h)
pdb|2AX0|A Chain A, Hepatitis C Virus Ns5b Rna Polymerase In Complex With A
Covalent Inhibitor (5x)
pdb|2AX0|B Chain B, Hepatitis C Virus Ns5b Rna Polymerase In Complex With A
Covalent Inhibitor (5x)
pdb|2AX1|A Chain A, Hepatitis C Virus Ns5b Rna Polymerase In Complex With A
Covalent Inhibitor (5ee)
pdb|2AX1|B Chain B, Hepatitis C Virus Ns5b Rna Polymerase In Complex With A
Covalent Inhibitor (5ee)
Length = 580
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|2BRK|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With An Allosteric Inhibitor (Compound 1)
pdb|2BRL|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With An Allosteric Inhibitor (Compound 2)
pdb|2WHO|A Chain A, Crystal Structure Of Hepatitis C Virus Ns5b Polymerase
From 1b Genotype In Complex With A Non-Nucleoside
Inhibitor
pdb|2WHO|B Chain B, Crystal Structure Of Hepatitis C Virus Ns5b Polymerase
From 1b Genotype In Complex With A Non-Nucleoside
Inhibitor
pdb|2WRM|A Chain A, Identification Of Novel Allosteric Inhibitors Of Hepatitis
C Virus Ns5b Polymerase Thumb Domain (Site Ii) By
Structure-Based Design
Length = 536
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|1YVF|A Chain A, Hepatitis C Virus Ns5b Rna-Dependent Rna Polymerase
Complex With Inhibitor Pha-00729145
pdb|1Z4U|A Chain A, Hepatitis C Virus Ns5b Rna-Dependent Rna Polymerase
Complex With Inhibitor Pha-00799585
Length = 577
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 68 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 104
>pdb|1NHU|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHU|B Chain B, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHV|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHV|B Chain B, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
Length = 578
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 75 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 111
>pdb|1QUV|A Chain A, Crystal Structure Of The Rna Directed Rna Polymerase Of
Hepatitis C Virus
pdb|2GC8|A Chain A, Structure Of A Proline Sulfonamide Inhibitor Bound To Hcv
Ns5b Polymerase
pdb|2GC8|B Chain B, Structure Of A Proline Sulfonamide Inhibitor Bound To Hcv
Ns5b Polymerase
pdb|2QE2|A Chain A, Structure Of Hcv Ns5b Bound To An Anthranilic Acid
Inhibitor
pdb|2QE2|B Chain B, Structure Of Hcv Ns5b Bound To An Anthranilic Acid
Inhibitor
pdb|2QE5|A Chain A, Structure Of Hcv Ns5b Bound To An Anthranilic Acid
Inhibitor
pdb|2QE5|B Chain B, Structure Of Hcv Ns5b Bound To An Anthranilic Acid
Inhibitor
pdb|2QE5|C Chain C, Structure Of Hcv Ns5b Bound To An Anthranilic Acid
Inhibitor
pdb|2QE5|D Chain D, Structure Of Hcv Ns5b Bound To An Anthranilic Acid
Inhibitor
pdb|3VQS|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase With A Novel
Piperazine Inhibitor
pdb|3VQS|B Chain B, Crystal Structure Of Hcv Ns5b Rna Polymerase With A Novel
Piperazine Inhibitor
pdb|3VQS|C Chain C, Crystal Structure Of Hcv Ns5b Rna Polymerase With A Novel
Piperazine Inhibitor
pdb|3VQS|D Chain D, Crystal Structure Of Hcv Ns5b Rna Polymerase With A Novel
Piperazine Inhibitor
Length = 578
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|4EO6|A Chain A, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
pdb|4EO6|B Chain B, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
pdb|4EO8|A Chain A, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
pdb|4EO8|B Chain B, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
Length = 577
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 74 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 110
>pdb|3MF5|A Chain A, Hepatitis C Virus Polymerase Ns5b (Bk) With Amide
Bioisostere Thumb Site Inhibitor
pdb|3MF5|B Chain B, Hepatitis C Virus Polymerase Ns5b (Bk) With Amide
Bioisostere Thumb Site Inhibitor
Length = 570
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|3HHK|A Chain A, Hcv Ns5b Polymerase Complex With A Substituted
Benzothiadizine
pdb|3HHK|B Chain B, Hcv Ns5b Polymerase Complex With A Substituted
Benzothiadizine
Length = 563
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|2WCX|A Chain A, Crystal Structure Of Hepatitis C Virus Ns5b Polymerase In
Complex With Thienopyrrole-Based Finger-Loop Inhibitors
pdb|2XWY|A Chain A, Structure Of Mk-3281, A Potent Non-Nucleoside Finger-Loop
Inhibitor, In Complex With The Hepatitis C Virus Ns5b
Polymerase
Length = 537
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 68 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 104
>pdb|2ZKU|A Chain A, Structure Of Hepatitis C Virus Ns5b Polymerase In A New
Crystal Form
pdb|2ZKU|B Chain B, Structure Of Hepatitis C Virus Ns5b Polymerase In A New
Crystal Form
pdb|2ZKU|C Chain C, Structure Of Hepatitis C Virus Ns5b Polymerase In A New
Crystal Form
pdb|2ZKU|D Chain D, Structure Of Hepatitis C Virus Ns5b Polymerase In A New
Crystal Form
pdb|3PHE|A Chain A, Hcv Ns5b With A Bound Quinolone Inhibitor
pdb|3PHE|B Chain B, Hcv Ns5b With A Bound Quinolone Inhibitor
pdb|3PHE|C Chain C, Hcv Ns5b With A Bound Quinolone Inhibitor
pdb|3PHE|D Chain D, Hcv Ns5b With A Bound Quinolone Inhibitor
pdb|3UDL|A Chain A, 3-Heterocyclyl Quinolone Bound To Hcv Ns5b
pdb|3UDL|B Chain B, 3-Heterocyclyl Quinolone Bound To Hcv Ns5b
pdb|3UDL|C Chain C, 3-Heterocyclyl Quinolone Bound To Hcv Ns5b
pdb|3UDL|D Chain D, 3-Heterocyclyl Quinolone Bound To Hcv Ns5b
Length = 576
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 73 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 109
>pdb|3BR9|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BR9|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSA|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSA|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSC|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSC|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CO9|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CO9|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CDE|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CDE|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CVK|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CVK|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CWJ|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CWJ|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3D28|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Benzisothiazole Inhibitor
pdb|3D28|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Benzisothiazole Inhibitor
pdb|3D5M|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3D5M|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3E51|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3E51|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3GYN|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydropyridinone Inhibitor
pdb|3GYN|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydropyridinone Inhibitor
pdb|3H2L|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase In Complex With A
Novel Bicyclic Dihydro-Pyridinone Inhibitor
pdb|3H2L|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase In Complex With A
Novel Bicyclic Dihydro-Pyridinone Inhibitor
pdb|3IGV|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydro-Pyridinone Inhibitor
pdb|3IGV|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydro-Pyridinone Inhibitor
Length = 578
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|3CIZ|A Chain A, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Small Molecule Fragments
pdb|3CIZ|B Chain B, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Small Molecule Fragments
pdb|3CJ0|A Chain A, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Small Molecule Fragments
pdb|3CJ0|B Chain B, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Small Molecule Fragments
pdb|3CJ2|A Chain A, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3CJ2|B Chain B, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3CJ3|A Chain A, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3CJ3|B Chain B, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3CJ4|A Chain A, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3CJ4|B Chain B, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3CJ5|A Chain A, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3CJ5|B Chain B, Crystal Structure Of Hepatitis C Virus Rna-Dependent Rna
Polymerase Ns5b In Complex With Optimized Small Molecule
Fragments
pdb|3FQK|A Chain A, Hepatitis C Virus Polymerase Ns5b (Bk 1-570) With Hcv-796
Inhibitor
pdb|3FQK|B Chain B, Hepatitis C Virus Polymerase Ns5b (Bk 1-570) With Hcv-796
Inhibitor
pdb|3G86|A Chain A, Hepatitis C Virus Polymerase Ns5b (Bk 1-570) With Thiazine
Inhibitor
pdb|3G86|B Chain B, Hepatitis C Virus Polymerase Ns5b (Bk 1-570) With Thiazine
Inhibitor
pdb|3H59|A Chain A, Hepatitis C Virus Polymerase Ns5b With Thiazine Inhibitor
2
pdb|3H59|B Chain B, Hepatitis C Virus Polymerase Ns5b With Thiazine Inhibitor
2
pdb|3H5S|A Chain A, Hepatitis C Virus Polymerase Ns5b With Saccharin Inhibitor
pdb|3H5S|B Chain B, Hepatitis C Virus Polymerase Ns5b With Saccharin Inhibitor
pdb|3H5U|A Chain A, Hepatitis C Virus Polymerase Ns5b With Saccharin Inhibitor
1
pdb|3H5U|B Chain B, Hepatitis C Virus Polymerase Ns5b With Saccharin Inhibitor
1
pdb|3H98|A Chain A, Crystal Structure Of Hcv Ns5b 1b With (1,1-Dioxo-2h-[1,2,
4]benzothiadiazin-3-Yl) Azolo[1,5-A]pyrimidine
Derivative
pdb|3H98|B Chain B, Crystal Structure Of Hcv Ns5b 1b With (1,1-Dioxo-2h-[1,2,
4]benzothiadiazin-3-Yl) Azolo[1,5-A]pyrimidine
Derivative
Length = 576
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 73 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 109
>pdb|2GIQ|A Chain A, Hepatitis C Virus Rna-Dependent Rna Polymerase Ns5b With
Nni-2 Inhibitor
pdb|2GIQ|B Chain B, Hepatitis C Virus Rna-Dependent Rna Polymerase Ns5b With
Nni-2 Inhibitor
pdb|2GIR|A Chain A, Hepatitis C Virus Rna-Dependent Rna Polymerase Ns5b With
Nni-1 Inhibitor
pdb|2GIR|B Chain B, Hepatitis C Virus Rna-Dependent Rna Polymerase Ns5b With
Nni-1 Inhibitor
Length = 568
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 73 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 109
>pdb|2JC0|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb655264
pdb|2JC0|B Chain B, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb655264
pdb|2JC1|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb698223
pdb|2JC1|B Chain B, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb698223
Length = 570
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|2FVC|A Chain A, Crystal Structure Of Ns5b Bk Strain (Delta 24) In Complex
With A 3-(1,1-Dioxo-2h-(1,2,4)-Benzothiadiazin-3-Yl)-4-
Hydroxy-2(1h)-Quinolinone
pdb|2FVC|B Chain B, Crystal Structure Of Ns5b Bk Strain (Delta 24) In Complex
With A 3-(1,1-Dioxo-2h-(1,2,4)-Benzothiadiazin-3-Yl)-4-
Hydroxy-2(1h)-Quinolinone
Length = 563
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|2DXS|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase Complexed
With A Tetracyclic Inhibitor
pdb|2DXS|B Chain B, Crystal Structure Of Hcv Ns5b Rna Polymerase Complexed
With A Tetracyclic Inhibitor
Length = 552
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
>pdb|2I1R|A Chain A, Novel Thiazolones As Hcv Ns5b Polymerase Inhibitors:
Further Designs, Synthesis, Sar And X-Ray Complex
Structure
pdb|2I1R|B Chain B, Novel Thiazolones As Hcv Ns5b Polymerase Inhibitors:
Further Designs, Synthesis, Sar And X-Ray Complex
Structure
pdb|2HWH|A Chain A, Hcv Ns5b Allosteric Inhibitor Complex
pdb|2HWH|B Chain B, Hcv Ns5b Allosteric Inhibitor Complex
pdb|2HWI|A Chain A, Hcv Ns5b Allosteric Inhibitor Complex
pdb|2HWI|B Chain B, Hcv Ns5b Allosteric Inhibitor Complex
pdb|2IJN|A Chain A, Isothiazoles As Active-Site Inhibitors Of Hcv Ns5b
Polymerase
pdb|2IJN|B Chain B, Isothiazoles As Active-Site Inhibitors Of Hcv Ns5b
Polymerase
pdb|2O5D|A Chain A, Thiazolone-Acylsulfonamides As Novel Hcv Ns5b Polymerase
Allosteric Inhibitors: Convergence Of Structure-Based
Drug Design And X-Ray Crystallographic Study
pdb|2O5D|B Chain B, Thiazolone-Acylsulfonamides As Novel Hcv Ns5b Polymerase
Allosteric Inhibitors: Convergence Of Structure-Based
Drug Design And X-Ray Crystallographic Study
Length = 576
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 73 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 109
>pdb|2D3U|A Chain A, X-Ray Crystal Structure Of Hepatitis C Virus Rna Dependent
Rna Polymerase In Complex With Non-Nucleoside Analogue
Inhibitor
pdb|2D3U|B Chain B, X-Ray Crystal Structure Of Hepatitis C Virus Rna Dependent
Rna Polymerase In Complex With Non-Nucleoside Analogue
Inhibitor
pdb|2D3Z|A Chain A, X-Ray Crystal Structure Of Hepatitis C Virus Rna-Dependent
Rna Polymerase In Complex With Non-Nucleoside Analogue
Inhibitor
pdb|2D3Z|B Chain B, X-Ray Crystal Structure Of Hepatitis C Virus Rna-Dependent
Rna Polymerase In Complex With Non-Nucleoside Analogue
Inhibitor
pdb|2D41|A Chain A, X-Ray Crystal Structure Of Hepatitis C Virus Rna-Dependent
Rna Polymerase In Complex With Non-Nucleoside Inhibitor
pdb|2D41|B Chain B, X-Ray Crystal Structure Of Hepatitis C Virus Rna-Dependent
Rna Polymerase In Complex With Non-Nucleoside Inhibitor
Length = 570
Score = 26.6 bits (57), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VLKNVEFKESDLKRDDISLEDLPLTIPPHHHKLQYQY 41
VLK ++ K S +K +S+E+ PPH K ++ Y
Sbjct: 67 VLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGY 103
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
0.322 0.137 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,405,789
Number of Sequences: 62578
Number of extensions: 208859
Number of successful extensions: 487
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 430
Number of HSP's gapped (non-prelim): 49
length of query: 173
length of database: 14,973,337
effective HSP length: 92
effective length of query: 81
effective length of database: 9,216,161
effective search space: 746509041
effective search space used: 746509041
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: 48 (23.1 bits)