Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1t57a_ | Hypothetical protein MTH1675 | PK C-terminal domain-like | Pyruvate kinase C-terminal domain-like | α/β |
| Hit | d1qv9a_ | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) | F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) | α/β |
Query <-- 0.668 --> IntermediateDALI alignment (Z-score: 4.8 Raw score:501.90) query 1 ---------dadeeVYSALVVGLRAYVAKNGFRSVLIGLSGgidsALVAAIACDALGaQN 51 ::::::::::::::::::::::::::: :::::::::::: :: d1t57a_ 1 mekkicyfeepgkeNTERVLELVGERADQLGIRNFVVASVS----GETALRLSEMVE-GN 55 query 52 VYGVSMPSK---YSSDhSKGD-AAELARRTGLNFRTVSI--ePMFDAYMASLGLtglaEE 105 ::::::::: :::: :::: ::::::::::::::::: :::::::::::: :: d1t57a_ 56 IVSVTHHAGfreKGQL-ELEDeARDALLERGVNVYAGSHalsGVGRGISNRFGG---vTP 111 query 106 NL----------qsrlrgTTLMAISNQ-------eGHIVLAPGnkselavgystlygdsV 148 :: ::::::::: :::::::: : d1t57a_ 112 VEimaetlrmvsqgfkvcVEIAIMAADaglipvdeEVIAIGGT-----------awgadT 160 query 149 GAYgpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtg 208 ::: d1t57a_ 161 ALV--------------------------------------------------------- 163 query 209 adaivaagydrelvvktlrmvdtaeykrrqyPPGTkisakgfgkdrrlpitnrwregh 266 :::: d1t57a_ 164 ----------------ltpahmnsvfdlrihEVIA-------------------mprp 186 FAST alignment (Normalized score: 3.32 Raw score:738.10) query 1 DAD------------EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDS--ALVAAIACDA 46 ::::::::::::::::::::::::::: :::::::::: d1t57a_ 1 ---MEKKICYFEEPGKENTERVLELVGERADQLGIRNFVVAS------VSGETALRLSEM 51 query 47 LGAQ--NVYGVSMPSKYSSDH-------------SKGDAAELARRTGLNFRTVSI----- 86 : :::::: ::::::::: ::::::::: d1t57a_ 52 V---EGNIVSVT---------HHAGFREKGQLELEDEARDALL-ERGVNVYAG--SHALS 96 query 87 EPMFDAYMASLGLTGLAEENLQ-----------------------SRLRGTTLMAI---- 119 ::::::::: :::::::::: d1t57a_ 97 GVGRGISNR-------------FGGVTPVEIMAETLRMVSQGFKVCVEIAIMAAD-AGLI 142 query 120 SNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQT 179 :::::::::: d1t57a_ 143 PVDEEVIAIG-------------------------------------------------- 152 query 180 PPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQY 239 d1t57a_ 153 ------------------------------------------------------------ 153 query 240 PPGTKISAKGFGKDRRLPITNRWREGH--------------------------------- 266 d1t57a_ 153 ---------------------------GTAWGADTALVLTPAHMNSVFDLRIHEVIAMPR 185 query 267 - 267 d1t57a_ 186 P 186 TMalign alignment (TM-score: 0.36 Raw score:96.37) query 1 ---------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACD 45 :::::::::::::::::::::::::: :: ::::::: d1t57a_ 1 MEKKICYFEEPGKEN------TERVLELVGERADQLGIRNFVVASVS---GE-TALRLSE 50 query 46 ALGAQNVYGVSMPSKYSS--DHSKGD-AAELARRTGLNFRTVSIEPMFDAYMASL-GLTG 101 ::: :::::::::::::: :::::: :::::::::::::::::::::::::::: ::: d1t57a_ 51 MVE-GNIVSVTHHAGFREKGQLELEDEARDALLERGVNVYAGSHALSGVGRGISNRFGG- 108 query 102 LAE--ENL--QSRL---------RG-TTLMA--I----SNQE-GHIVLAPGNKSELAVGY 140 :: : :: :: ::::: : :::: :::::::: d1t57a_ 109 -VTPV--EIM--AETLRMVSQGFKVCVEIAIMAADAGLIPVDEEVIAIGGT--------- 154 query 141 STLYGDSVGAY----------------GPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPE 184 ::: :::::: d1t57a_ 155 -AWG-ADTALVLTPAHMNSVFDLRIHE--------------------------------- 179 query 185 ASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTK 244 :::: d1t57a_ 180 ------------------------------------------------------VIAM-- 183 query 245 ISAKGFGKDRRLPITNRWREGH 266 : : : d1t57a_ 184 -----P-R-----P-------- 186 HHsearch alignment (Probability: 0.08 E-value:0.04) query 16 AYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELAR 75 :::::::::::::::::: :::::::::: ::::::::::::::::::::::::::: d1t57a_ 25 ERADQLGIRNFVVASVSG----ETALRLSEMV-EGNIVSVTHHAGFREKGQLELEDEARD 79 query 76 RT 77 :: d1t57a_ 80 AL 81
Intermediate <-- 1.348 --> HitDALI alignment (Z-score: 3.9 Raw score:397.70) d1t57a_ 1 ------------------------------mekkicyfeePGKE--NTERVLELVGERAD 28 :::: :::::::::::::: d1qv9a_ 1 tvakaifikcgnlgtsmmmdmllderadredvefrvvgtsVKMDpeCVEAAVEMALDIAE 60 d1t57a_ 29 QLGIRNFVVASVSG------eTALRLSEmVEGNIVSVTHhagfrekgqLELEDeARDALL 82 :::::::::::::: ::::::: :::::::::: ::::: :::::: d1qv9a_ 61 DFEPDFIVYGGPNPaapgpskAREMLAD-SEYPAVIIGD---------APGLK-VKDEME 109 d1t57a_ 83 ERGVNVYAGSH-----------------------alSGVGRGisnrfggvtpveimaetl 119 ::::::::::: :::::: d1qv9a_ 110 EQGLGYILVKPdamlgarrefldpvemaiynadlmkVLAATG------------------ 151 d1t57a_ 120 rmvsqgfkvcveiaimaADAG-lIPVDEE------------------------------- 147 :::: :::::: d1qv9a_ 152 ------------vfrvvQEAFdeLIEKAKedeisendlpklvidrntllereefenpyam 199 d1t57a_ 148 ------------------------------------------viaiggtawgadtalvlt 165 d1qv9a_ 200 vkamaaleiaenvadvsvegcfveqdkeryvpivasahemmrkaaeladeareleksnda 259 d1t57a_ 166 pahmNSVFDL--riheviamprp 186 :::::: d1qv9a_ 260 vlrtPHAPDGkvlskrkfmedpe 282 FAST alignment (Normalized score: 2.71 Raw score:620.40) d1t57a_ 1 MEKKICYFEEP-------------------------------------------GKENTE 17 :::::: d1qv9a_ 1 -----------TVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVE 49 d1t57a_ 18 RVLELVGERADQLGIRNFVVASVS------GETALRLSEMVEGNIVSVTHHAGFREKGQL 71 :::::::::::::::::::::::: :::::::: :::::::::: d1qv9a_ 50 AAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLA-DSEYPAVIIG----------- 97 d1t57a_ 72 EL---EDEARDALLERGVNVYAGSHALSGVGRGISNRFGGV----------------TPV 112 ::::::::::::::::: ::: d1qv9a_ 98 --DAPGLKVKDEMEEQGLGYIL-------------------VKPDAMLGARREFLDPVEM 136 d1t57a_ 113 EIMAETLRMVSQGFKVCVEI--------AIMAADAGLIPVDEEVIAIGGTAWGADTALVL 164 :::::::: :::: d1qv9a_ 137 AIYNADLM------------KVLAATGVFRVV---------------------------- 156 d1t57a_ 165 TPAHMNSVFDLRIHEVIAMPRP-------------------------------------- 186 d1qv9a_ 157 ----------------------QEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFE 194 d1t57a_ 187 ------------------------------------------------------------ 187 d1qv9a_ 195 NPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELE 254 d1t57a_ 187 ---------------------------- 187 d1qv9a_ 255 KSNDAVLRTPHAPDGKVLSKRKFMEDPE 282 TMalign alignment (TM-score: 0.42 Raw score:77.87) d1t57a_ 1 -----------------------------------MEKKICYFEEPGKE--NTERVLELV 23 :::: ::::: ::::::::: d1qv9a_ 1 TVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFR----VVGT-SVKMDPECVEAAVEMA 55 d1t57a_ 24 GERADQLGIRNFVVASVSGE---T--ALRLSEMVEGNIVSVTHHAGFREKGQLELEDEAR 78 :::::::::::::::::::: : ::::::::::::::::: ::::: :: d1qv9a_ 56 LDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGD---------APGLK-VK 105 d1t57a_ 79 DALLERGVNVYAGSHA-----------------LSGVGRGISNRFG-GVT-PVEI-MA-- 116 :::::::::::::::: : :: ::: : d1qv9a_ 106 DEMEEQGLGYILVKPDAMLGARREFLDPVEMAI------------YN-ADL-MKVL-AAT 150 d1t57a_ 117 -ETLRMVSQGFKVCVEIAIMAADAG-LIPV-DE--------------------------- 146 :: ::::::: :::: :: d1qv9a_ 151 G--------------VF-RVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFEN 195 d1t57a_ 147 ------------------------------------------------------------ 147 d1qv9a_ 196 PYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEK 255 d1t57a_ 147 ------EVIAIGGTAWGADTALVLTPAHMNSVFD-LR-------------IHEVIAMPRP 186 :::::: : d1qv9a_ 256 SNDAVL----------------------RTPHAPD-GKVLSKRKFMEDPE---------- 282 HHsearch alignment (Probability: 0.05 E-value:0.09) d1t57a_ 11 PGKENTERVLELVGERADQLGIRNFVVASVSG-----ETALRLSEMVEGNIVSVTHHAGF 65 :::::::::::::::::::::::::::::::: :::::::::::::::::::::: d1qv9a_ 43 MDPECVEAAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPG- 101 d1t57a_ 66 REKGQLELEDEARDALLERGVN-VYAGSHALSGVGRGISNRFGGVTPVEIM---AETLRM 121 ::::::::::::: ::::::::::::::: ::::::: :::::: d1qv9a_ 102 ---------LKVKDEMEEQGLGYILVKPDAMLGARREF------LDPVEMAIYNADLMKV 146 d1t57a_ 122 VSQ-G----FKVCVEIAIMAADAGLIPV 144 ::: : ::::::::::::::::::: d1qv9a_ 147 LAATGVFRVVQEAFDELIEKAKEDEISE 174