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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jx7a_ | Hypothetical protein YchN | YchN-like | YchN-like | α/β |
| Hit | d1pixa1 | Glutaconyl-CoA decarboxylase A subunit | ClpP/crotonase | ClpP/crotonase | α/β |
Query <-- 1.887 --> IntermediateDALI alignment (Z-score: 13.0 Raw score:806.90) query 1 gmeNKKMNLLLFSGDY--DKALASLIIANAAREME--IEVTIFCAFWGLLLLRDPekasq 56 ::::::::::::: ::::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYgsESLFNSLRLAIALREQEsnLDLRLFLMSDAVTAGLRG----- 52 query 57 edkslyeqafssltpreaeelplskmnlggigkkmlLEMMkeekaPKLSDLLSGARKKEV 116 :::: ::::::::::::::: d1jx7a_ 53 ----------------------------------qkPGEG-----YNIQQMLEILTAQNV 73 query 117 KFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 74 PVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 FAST alignment (Normalized score: 12.96 Raw score:1774.00) query 1 GMENKKMNLLLFSGD---YDKALASLIIANAARE--MEIEVTIFCAFWGLLLLRDPEKAS 55 ::::::::::: :::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGA-PYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGL------ 50 query 56 QEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEE------KAPKLSDLLS 109 :::::::::: d1jx7a_ 51 --------------------------------------------RGQKPGEGYNIQQMLE 66 query 110 GARKKEVKFYAXQLSVEIMGFKKE-ELFPEVQIMDVKEYLKNALESDLQLFI-- 160 :::::::::::::::::::: ::: ::::::::::::::::::::::::: d1jx7a_ 67 ILTAQNVPVKLCKTCTDGRG-ISTLPLIDGVEIGTLVELAQWTLSADKVL--TF 117 TMalign alignment (TM-score: 0.61 Raw score:97.67) query 1 GMENKKMNLLLFSGDY--DKALASLIIANAARE-M-EIEVTIFCAFWGLLLLRDPEKASQ 56 ::::::::::::: ::::::::::::::: : ::::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRG----- 52 query 57 EDKSLYEQAFSSLTPREAEE-LPLSKMNLGGIGKKMLLEMMKEEKAPKLS-DLLSGARKK 114 : :: : : ::: ::::::::: d1jx7a_ 53 ----------------Q-KPG-------------E--G---------YNIQQMLEILTAQ 71 query 115 EVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 72 NVPVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 HHsearch alignment (Probability: 0.99 E-value:0.00) query 5 KKMNLLLFSG--DYDKALASLIIANAAREMEI--EVTIFCAFWGLLLLRDPEKASQEDKS 60 :::::::::: :::::::::::::::::::: ::::::::::::::::::::: d1jx7a_ 2 QKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRGQKPG----- 56 query 61 LYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYA 120 ::::::::::::::::::::: d1jx7a_ 57 ---------------------------------------EGYNIQQMLEILTAQNVPVKL 77 query 121 XQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQL 158 :::::::::::::::::::::::::::::::::::::: d1jx7a_ 78 CKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVL 115
Intermediate <-- 0.643 --> HitDALI alignment (Z-score: 4.0 Raw score:342.10) d1jx7a_ 1 ------------------------------------------------------------ 1 d1pixa1 1 gfysmpryfqnmpqvgkplkkadaaneeqlkkieeeihqlikeaqeagkadadvnkrgel 60 d1jx7a_ 1 -----------------------------------------mQKIVIVANG--------- 10 ::::::::: d1pixa1 61 talqrieklvepgswrplntlfnpqgnkngsvaivkglgrvnGKWCVVVASdnkklagaw 120 d1jx7a_ 11 apYGSESLFNSLRLAIALReqesnldLRLFLMSD--avtaglrgqkPGEGY---NIQQML 65 ::::::::::::::::: :::::::: ::::: :::::: d1pixa1 121 vpGQAECLLRASDTAKTLH-------VPLVYVLNcsgvkfdeqekvYPNRRgggTPFFRN 173 d1jx7a_ 66 EILTAQNVPVKLCKTctDGRG-istlplidgVEIG------------------------- 99 ::::::::::::::: :::: :::: d1pixa1 174 AELNQLGIPVIVGIY--GTNPagggyhsispTVIIahekanmavggagimggmnpkghvd 231 d1jx7a_ 100 ------------------------------------------TLVELAQWTLS------- 110 ::::::::::: d1pixa1 232 leyaneiadmvdrtgkteppgavdihytetgfmrevyaseegVLEGIKKYVGMlpkydpe 291 d1jx7a_ 111 ------------------------------------------------------------ 111 d1pixa1 292 ffrvddpkapafpaddlysmvplndkraydiynviarlfdnselheykkgygpemvtgla 351 d1jx7a_ 111 ------------------------------------------------------------ 111 d1pixa1 352 kvngllvgvvanvqgllmnypeykaagsvgiggklyrqglvkmnefvtlcardrlpivwi 411 d1jx7a_ 111 ------------------------------------------------------------ 111 d1pixa1 412 qdttgidvgndaekaellglgqsliysiqtshipqfeitlrkgtaaahyvlggpqgndtn 471 d1jx7a_ 111 ------------------------------------------------------------ 111 d1pixa1 472 afsigtaateiavmngetaatamysrrlakdrkagkdlqptidkmnnliqafytksrpkv 531 d1jx7a_ 111 ------------------------------------------------adkvltf 117 d1pixa1 532 caelglvdeivdmnkirgyveafteaayqnpesicpfhqmilprairefetfvkk 586 FAST alignment (Normalized score: 1.70 Raw score:444.70) d1jx7a_ 1 MQ---------------------------------------------------------- 2 d1pixa1 1 --GFYSMPRYFQNMPQVGKPLKKADAANEEQLKKIEEEIHQLIKEAQEAGKADADVNKRG 58 d1jx7a_ 3 ---------------------------------------------KIVIVANGAPYGS-- 15 :::::: d1pixa1 59 ELTALQRIEKLVEPGSWRPLNTLFNPQGNKNGSVAIVKGLGRVNGKWCVVV-------AS 111 d1jx7a_ 16 ----------ESLFNSLRLAIALREQESNLD-LRLFLMSDAVTAGLRGQK---------- 54 ::::::::::::::::: ::::: d1pixa1 112 DNKKLAGAWVPGQAECLLRASDTAKTL----HVPLVY-------------VLNCSGVKFD 154 d1jx7a_ 55 -----PGEGY---NIQQMLEILTAQNVPVKLCKTCTDGRGISTLPLIDG----------- 95 ::::: ::::::::::::::::::: d1pixa1 155 EQEKVYPNRRGGGTPFFRNAELNQLGIPVIVG-----------------IYGTNPAGGGY 197 d1jx7a_ 96 -----VEIG--------------------------------------------------- 99 :::: d1pixa1 198 HSISPTVIIAHEKANMAVGGAGIMGGMNPKGHVDLEYANEIADMVDRTGKTEPPGAVDIH 257 d1jx7a_ 100 ----------------TLVELAQWTLSADKVLTF-------------------------- 117 ::::::::::: d1pixa1 258 YTETGFMREVYASEEGVLEGIKKYVGM-------LPKYDPEFFRVDDPKAPAFPADDLYS 310 d1jx7a_ 118 ------------------------------------------------------------ 118 d1pixa1 311 MVPLNDKRAYDIYNVIARLFDNSELHEYKKGYGPEMVTGLAKVNGLLVGVVANVQGLLMN 370 d1jx7a_ 118 ------------------------------------------------------------ 118 d1pixa1 371 YPEYKAAGSVGIGGKLYRQGLVKMNEFVTLCARDRLPIVWIQDTTGIDVGNDAEKAELLG 430 d1jx7a_ 118 ------------------------------------------------------------ 118 d1pixa1 431 LGQSLIYSIQTSHIPQFEITLRKGTAAAHYVLGGPQGNDTNAFSIGTAATEIAVMNGETA 490 d1jx7a_ 118 ------------------------------------------------------------ 118 d1pixa1 491 ATAMYSRRLAKDRKAGKDLQPTIDKMNNLIQAFYTKSRPKVCAELGLVDEIVDMNKIRGY 550 d1jx7a_ 118 ------------------------------------ 118 d1pixa1 551 VEAFTEAAYQNPESICPFHQMILPRAIREFETFVKK 586 TMalign alignment (TM-score: 0.53 Raw score:62.47) d1jx7a_ 1 ------------------------------------------------------------ 1 d1pixa1 1 GFYSMPRYFQNMPQVGKPLKKADAANEEQLKKIEEEIHQLIKEAQEAGKADADVNKRGEL 60 d1jx7a_ 1 ------------------------------------------MQKI-VIVAN-----GAP 12 :::: ::::: ::: d1pixa1 61 TALQRIEKLVEPGSWRPLNTLFNPQGNKNGSVAIVKGLGRVNGKWCVVVASDNKKLAGAW 120 d1jx7a_ 13 YGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTA-------GLRGQKPGEGYNIQQML 65 ::: :::::::::::::::: :::::::: :::: ::: ::::::::: d1pixa1 121 -VPG-QAECLLRASDTAKTLH-VPLVYVLN--CSGVKFDEQEK----VYP-NRRGGGTPF 170 d1jx7a_ 66 EILTAQN-----VPVKLCKTCTDGRGIS-TLPLI--DGV--EIGT--------------- 100 ::::::: :::::: :: : :: ::: ::: :::: d1pixa1 171 FRNAELNQLGIPVIVGIY--GT--N-PAG--GGYHSISPTVIIAHEKANMAVGGAGIMGG 223 d1jx7a_ 101 -----------------------------------------------L-VELAQ-WTL-S 110 : ::: : ::: : d1pixa1 224 MNPKGHVDLEYANEIADMVDRTGKTEPPGAVDIHYTETGFMREVYASEEGVL-EGIKKYV 282 d1jx7a_ 111 A----------------------------------------------------------- 111 : d1pixa1 283 GMLPKYDPEFFRVDDPKAPAFPADDLYSMVPLNDKRAYDIYNVIARLFDNSELHEYKKGY 342 d1jx7a_ 112 ------------------------------------------------------------ 112 d1pixa1 343 GPEMVTGLAKVNGLLVGVVANVQGLLMNYPEYKAAGSVGIGGKLYRQGLVKMNEFVTLCA 402 d1jx7a_ 112 ------------------------------------------------------------ 112 d1pixa1 403 RDRLPIVWIQDTTGIDVGNDAEKAELLGLGQSLIYSIQTSHIPQFEITLRKGTAAAHYVL 462 d1jx7a_ 112 ------------------------------------------------------------ 112 d1pixa1 463 GGPQGNDTNAFSIGTAATEIAVMNGETAATAMYSRRLAKDRKAGKDLQPTIDKMNNLIQA 522 d1jx7a_ 112 ------------------------------DK---------------------------- 113 : d1pixa1 523 FYTKSRPKVCAELGLVDEIVDMNKIRGYVE-AFTEAAYQNPESICPFHQMILPRAIREFE 581 d1jx7a_ 114 -----VLTF 117 d1pixa1 582 TFVKK---- 586 HHsearch alignment (Probability: 0.02 E-value:0.29) d1jx7a_ 61 IQQMLEILTAQNVP 74 :::::::::::::: d1pixa1 432 GQSLIYSIQTSHIP 445