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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1knwa1 | Diaminopimelate decarboxylase LysA | Alanine racemase C-terminal domain-like | Domain of alpha and beta subunits of F1 ATP synthase-like | All β |
| Hit | d1hh2p1 | S1 domain of NusA | Nucleic acid-binding proteins | OB-fold | All β |
Query <-- 1.321 --> IntermediateDALI alignment (Z-score: 15.0 Raw score:988.00) query 1 ---------------------MIETPYYLIdkakltrnmeriahvreksgakallalkcf 39 ::::::::: d1knwa1 1 phslfstdtdltaenllrlpaEFGCPVWVY------------------------------ 30 query 40 atwsvfdlmrdymdgttssslfevrlgrerfgkethaysvaygdneidevvshadkiifn 99 d1knwa1 31 ------------------------------------------------------------ 31 query 100 sisqlerfadkaagiarglrlnpqrlgewdvpkvervmdringfmihnncenkdfglfdr 159 d1knwa1 31 ------------------------------------------------------------ 31 query 160 mlgeieerfgaliarvdwvslgggihftgddypvdafsarlrafsdrygvqiylepgeas 219 d1knwa1 31 ------------------------------------------------------------ 31 query 220 itkstTLEVTVLDTLYN--KNLAIVDSSIeAHMLDLLIYRETAKVL---------pneGS 268 :::::::::::: :::::::::: :::::::::::::::: :: d1knwa1 31 -----VLITQVRSVKQMgsRHFVLVDAGF-NDLMRPAMYGSYHHISalaadgrslehaPT 84 query 269 HSYMICGKSCLAGDVFG--------EFRFaEELKVGDRISFQDAAGYTMVKKNWFNGVKM 320 ::::::::::::::::: :::: :::::::::::::::::::::::::::::: d1knwa1 85 VETVVAGPLCESGDVFTqqeggnveTRAL-PEVKAGDYLVLHDTGAYGASMSSNYNSRPL 143 query 321 PAIAIRELdGSVRTVREFTYadYEQSLS------ 348 :::::::: ::::::::::: :::::: d1knwa1 144 LPEVLFDN-GQARLIRRRQT--IEELLAlellhh 174 FAST alignment (Normalized score: 8.04 Raw score:1978.00) query 1 ---------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF 39 ::::::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVW-------------------------------- 28 query 40 ATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFN 99 d1knwa1 29 ------------------------------------------------------------ 29 query 100 SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDR 159 d1knwa1 29 ------------------------------------------------------------ 29 query 160 MLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 d1knwa1 29 ------------------------------------------------------------ 29 query 220 ITKS-TTLEVTVLDTLYN----KNLAIVDSSIEAHMLDLLIYRETAKVLPNEG------- 267 ::::::::::: ::::::::: :::::::::::::::: d1knwa1 29 ----VYVLITQVRSVK--QMGSRHFVLVDAG-FNDLMRPAMYGSYHHI-----SALAADG 76 query 268 -------SHSYMICGKSCLAGDV--------FGEFRFAEELKVGDRISFQDAAGYTMVKK 312 :::::::::::::::: :::::: :::::::::::::::::::::: d1knwa1 77 RSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRAL-PEVKAGDYLVLHDTGAYGASMS 135 query 313 NWFNGVKMPAIAIRELDGSVRTV-REFTYADYEQSLS----- 348 ::::::::::::::: ::::::: ::::::::::: d1knwa1 136 SNYNSRPLLPEVLFD-NGQARLIRRRQTIEELLAL--ELLHH 174 TMalign alignment (TM-score: 0.35 Raw score:120.59) query 1 ---------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF 39 ::::::::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVY------------------------------ 30 query 40 ATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFN 99 d1knwa1 31 ------------------------------------------------------------ 31 query 100 SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDR 159 d1knwa1 31 ------------------------------------------------------------ 31 query 160 MLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 d1knwa1 31 ------------------------------------------------------------ 31 query 220 ITKSTTLEVTVLDTLYN--KNLAIVDSSIEAHMLDLLIYRETAKVLP--------NE-GS 268 :::::::::::: :::::::::: ::::::::::::::::: :: :: d1knwa1 31 -----VLITQVRSVKQMGSRHFVLVDAGF-NDLMRPAMYGSYHHISALAADGRSLEHAPT 84 query 269 HSYMICGKSCLAGDVFG--------EFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKM 320 ::::::::::::::::: ::::: ::::::::::::::::::::::::::::: d1knwa1 85 VETVVAGPLCESGDVFTQQEGGNVETRALP-EVKAGDYLVLHDTGAYGASMSSNYNSRPL 143 query 321 PAIAIRELDGSVRTVRE-FTYADYEQSLS--- 348 :::::::: :::::::: ::::::::::: d1knwa1 144 LPEVLFDN-GQARLIRRRQTIEELLALELLHH 174 HHsearch alignment (Probability: 1.00 E-value:0.00) query 193 VDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLD 252 ::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::: d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYVLITQVRSVKQMGSRHFVLVDAGFN-DLMR 59 query 253 LLIYRETAKVLP---------NEGSHSYMICGKSCLAGDVFGEF-------RFAEELKVG 296 :::::::::::: ::::::::::::::::::::::: ::::::::: d1knwa1 60 PAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAG 119 query 297 DRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 :::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa1 120 DYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLAL 169
Intermediate <-- 0.590 --> HitDALI alignment (Z-score: 0.8 Raw score:120.10) d1knwa1 1 phslfstdtdltaenllrlpaefgcpvwvyVLITQVRSVKQmgsrHFVLVDAGfndlmrp 60 ::::::::::: :::::::: d1hh2p1 1 --------------------fekyselkgtVTTAEVIRVMG----EWADIRIG------- 29 d1knwa1 61 amygsyhhisalaadgrslehaptvetvvagplcesgdvftqqeggnveTRAL--PEVKA 118 :::: ::::: d1hh2p1 30 -----------------------------------------kletrlpkKEWIpgEEIKA 48 d1knwa1 119 GDYLVLHdTGAYgasMSSNYNsrpllpevlfdngqarlirrrqtieellalellhh 174 ::::::: :::: :::::: d1hh2p1 49 GDLVKVY-IIDV---VKTTKG----------------------------pkilvsr 72 FAST alignment (Normalized score: 1.59 Raw score:178.10) d1knwa1 1 PHSLFSTDTDLTAENLLRLPAEFGCPVWV---------YVLITQVRSVKQMGSR-HFVLV 50 ::::::::::: ::::: d1hh2p1 1 -----------------------------FEKYSELKGTVTTAEVIRVM-----GEWADI 26 d1knwa1 51 DAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVET 110 : d1hh2p1 27 R----------------------------------------------------------- 27 d1knwa1 111 RAL----------------PEVKAGDYLVLHDTGAYG-ASMSSNYNSRPLLPEVLFDNGQ 153 ::::::::::: :::::: d1hh2p1 28 ---IGKLETRLPKKEWIPGEEIKAGDLVKV-------YIIDVVK---------------- 61 d1knwa1 154 ARLIRRRQTIEELLALELLHH----------- 174 d1hh2p1 62 ---------------------TTKGPKILVSR 72 TMalign alignment (TM-score: 0.14 Raw score:24.72) d1knwa1 1 ----PHSLFSTDTDLTAENLLRLPAEFGCPVWVYVLITQVRSVKQMGSRHFVLVDAGFND 56 : d1hh2p1 1 FEKY---------------------------------------------S---------- 5 d1knwa1 57 LMRPAMYGSYHHISALAADGRSLEHAPT-VET-V-VAGPLCESGD---V----------- 99 ::: ::: : : :::: : d1hh2p1 6 -------------------------ELKGTVTTAE-V----IRVMGEWADIRIGKLETRL 35 d1knwa1 100 F--TQQ--EGG---N-VETRALPEVKAG--DYLV---LHDTGAYGASMSSNYNSRPLLPE 146 : ::: ::: : :::::::::::: :::: d1hh2p1 36 PKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSR----------------------- 72 d1knwa1 147 VLFDNGQARLIRRRQTIEELLALELLHH 174 d1hh2p1 73 ---------------------------- 73 HHsearch alignment (Probability: 0.01 E-value:0.23) d1knwa1 42 MGSRHFVLVDAGFNDLMRP 60 ::::::::::::::::::: d1hh2p1 18 RVMGEWADIRIGKLETRLP 36