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 | d1a49a2 | Pyruvate kinase, N-terminal domain | Phosphoenolpyruvate/pyruvate domain | TIM beta/alpha-barrel | α/β |
| Hit | d1rkda_ | Ribokinase | Ribokinase-like | Ribokinase-like | α/β |
Query <-- 0.742 --> IntermediateDALI alignment (Z-score: 11.1 Raw score:1131.40) query 1 ---mietpyylidkakltrnmeriahvreKSGAKALLALKC-FATWSVFDLMRD-YMDGT 55 :::::::::::: :::::::::::: ::::: d1a49a2 1 iqtqqlhaamadtflehmcrldidsapitARNTGIICTIGPaSRSVETLKEMIKsGMNVA 60 query 56 TSSS----LFEVRLGRERFG---------------KETHAYSVA-----yGDNEIDEVVS 91 :::: :::::::::::: ::::::::: :::::::::: d1a49a2 61 RMNFshgtHEYHAETIKNVRtatesfasdpilyrpVAVALDTKGpavsekDIQDLKFGVE 120 query 92 H-ADKIIFNS---ISQLERFADKA----AGIARGLRLNPQrlgEWDVpkVERVMDRINGF 143 : :::::::: ::::::::::: :::::::::::: :::: ::::::::::: d1a49a2 121 QdVDMVFASFirkAADVHEVRKILgekgKNIKIISKIENH--eGVRR--FDEILEASDGI 176 query 144 MIHNNcenkdfglfdRMLGEIEeRFGALIA-RVDWVSLGGGIHFTG--DDYPVDAFSARL 200 ::::: ::::::: ::::::: ::::::::::::::: :::::::::::: d1a49a2 177 MVARG-dlgieipaeKVFLAQK-MIIGRCNrAGKPVICATQMLESMikKPRPTRAEGSDV 234 query 201 RAFSDRYgvQIYLEPGEAS-ITKSttlevtvldtlynknlaivdssieahmldlliyret 259 ::::::: :::::::::: :::: d1a49a2 235 ANAVLDG--ADCIMLSGETaKGDY------------------------------------ 256 query 260 akvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvk 319 d1a49a2 257 ------------------------------------------------------------ 257 query 320 mpaiaireldgsvrtvreftyadyeqsls 348 d1a49a2 257 ---pleavrmqhliareaeaamfhrklfe 282 FAST alignment (Normalized score: 5.85 Raw score:1832.00) query 1 MIETPYYLIDKAKLTRNMERIAHVRE-----------------------------KSGAK 31 ::::: d1a49a2 1 --------------------------IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTG 34 query 32 ALLAL-KCFATWSVFDLMRD-YMDGTTSS---------SLFEVRLGRERFG--------- 71 ::::: :::::::::::::: ::::::: :::::::::: d1a49a2 35 IICTIGPASRSVETLKEMIKSGMNVARM-NFSHGTHEYHAETIKNVRT---ATESFASDP 90 query 72 -----KETHAYSVAY--------GDNEIDEVVS-HADKIIFN---SISQLERFADK---- 110 ::::::: :::::::::: :::::::: ::::::::::: d1a49a2 91 ILYRPVAVALDT---KGPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKILGEK 147 query 111 AAGIARGLRLNPQRLGEW----DVPKVERVMDRINGFMIHNNCENKDFGLFDRM------ 160 :::::::::: :::::::::::::::::: d1a49a2 148 GKNIKIISKI--------ENHEGVRRFDEILEASDGIMVA--------------RGDLGI 185 query 161 ---LGEIEERFGALIARV-----DWVSLGGGIHFTGDDYP-----------VDAFSARLR 201 :::::::::::::: :::::::: ::::::::: d1a49a2 186 EIPAEKVFLAQKMIIGR-CNRAGKPVICATQ---------MLESMIKKPRPTRAEGSDVA 235 query 202 AFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAK 261 :::: ::: :::::::: d1a49a2 236 NAVL-DGA-DCIMLSGE------------------------------------------- 250 query 262 VLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMP 321 d1a49a2 251 ------------------------------------------------------------ 251 query 322 AIAIRELDGSVRTVREFTYADYEQSLS-------------------------------- 348 d1a49a2 251 ---------------------------TAKGDYPLEAVRMQHLIAREAEAAMFHRKLFE 282 TMalign alignment (TM-score: 0.44 Raw score:151.70) query 1 --------------------------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALL 34 ::::::::::: d1a49a2 1 IQTQQLHAAMADTFLEHMCRLDIDSA-----------------------PITARNTGIIC 37 query 35 ALKCFATWS-VFDLMRDY-MDGTTSSS----LFEVRLGRERFG---------------KE 73 ::::::::: :::::::: :::::::: :::::::::::: :: d1a49a2 38 TIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVA 97 query 74 THAYSVA-----YGDNEIDEVV-SHADKIIFN-S-I-SQLERFAD-K---AAGIARGLRL 120 ::::::: :::::::::: ::::::::: : : :::::::: : :::::::::: d1a49a2 98 VALDTKGPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKILGEKGKNIKIISKI 157 query 121 NPQRLGEWDVPKVERVMDRINGFMIHNNC-EN----KDFGLFDRMLGEIEERFGALIA-R 174 ::: ::::: ::::::::::::::::: : :::::::::: :::::: : d1a49a2 158 ENH--EGVRR--FDEILEASDGIMVARGDL-GIEIP-----AEKVFLAQKM-IIGRCNRA 206 query 175 VDWVSLGGGIHF-T--G-DDYP-VDAFSARLRAFSDRYGVQIYLEPGEASITKST----- 224 :::::::::::: : : :::: :::::::::::: :::::::::::::::: d1a49a2 207 GKPVICATQMLESMIKKPRPTRAEGSDVANAVLDG----ADCIMLSGETAKGDYPLEAVR 262 query 225 --------------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLP 264 d1a49a2 263 MQHLIAREAEAAMFHRKLFE---------------------------------------- 282 query 265 NEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIA 324 d1a49a2 283 ------------------------------------------------------------ 283 query 325 IRELDGSVRTVREFTYADYEQSLS 348 d1a49a2 283 ------------------------ 283 HHsearch alignment (Probability: 0.10 E-value:0.08) query 82 GDNEIDEVVSHADKII-FN----SISQLERFADKAAGI------------ARGLRLNPQR 124 :::::::::::::::: :: ::::::::::::::: :::::::::: d1a49a2 45 SVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKG 104 query 125 LGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWV 178 :::::::::::::::::::::::::::::::: :::::::::::::::::: d1a49a2 105 PAVSEKDIQDLKFGVEQDVDMVFASFIRKAAD----VHEVRKILGEKGKNIKII 154
Intermediate <-- 0.631 --> HitDALI alignment (Z-score: 2.7 Raw score:420.70) d1a49a2 1 iqtqqlhaamadtflehmcrldidsapitarntgiictigpasrsvetlkemiksgmnva 60 d1rkda_ 1 ------------------------------------------------------------ 1 d1a49a2 61 rmnfshgtheyhaetiknvrtatesfasdpilyrpvavaldtkgpavsekdiqdlkfgve 120 d1rkda_ 1 ------------------------------------------------------------ 1 d1a49a2 121 qdvdmvfasfirkaadvhevrkilgekgknIKIISKIENH-------------------- 160 :::::::::: d1rkda_ 1 ------------------------------AGSLVVLGSInadhilnlqsfptpgetvtg 30 d1a49a2 161 ------------------------------------------------------------ 161 d1rkda_ 31 nhyqvafggkganqavaagrsganiafiactgddsigesvrqqlatdniditpvsvikge 90 d1a49a2 161 -----------------------------egVRRFDEILEASDGIMVARGDlgieipaek 191 :::::::::::::::::::: d1rkda_ 91 stgvalifvngegenvigihaganaalspalVEAQRERIANASALLMQLES--------- 141 d1a49a2 192 VFLAQKMIIGRCNRAGKPVICATQmlesmikkprptraegSDVANAVLdGADCIMLSGE- 250 :::::::::::::::::::::::: :::::::: :::::::::: d1rkda_ 142 PLESVMAAAKIAHQNKTIVALNPA-------------parELPDELLA-LVDIITPNETe 187 d1a49a2 251 -----takgDYPLEAVRMqHLIAREAE--------------------------------- 272 ::::::::: :::::::: d1rkda_ 188 aekltgirvENDEDAAKA-AQVLHEKGirtvlitlgsrgvwasvngegqrvpgfrvqavd 246 d1a49a2 273 --------------------------------------------------aamfhrklfe 282 d1rkda_ 247 tiaagdtfngalitalleekplpeairfahaaaaiavtrkgaqpsvpwreeidafldrqr 306 FAST alignment (Normalized score: 1.98 Raw score:582.70) d1a49a2 1 IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASR---------------- 44 d1rkda_ 1 --------------------------------------------AGSLVVLGSINADHIL 16 d1a49a2 45 ------------------------------------------------------------ 45 d1rkda_ 17 NLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLAT 76 d1a49a2 45 ------------------------------------------------SVETLKEMIKSG 56 ::::::: d1rkda_ 77 DNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIAN----- 131 d1a49a2 57 MNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPAVSEKDIQDLK 116 :::::::: :::::::::::::::: :::::::: d1rkda_ 132 ASALLMQL-ESPLESVMAAAKIAHQ------------NKTIVALN--------------- 163 d1a49a2 117 FGVEQ-------------DVDMVFAS-----------FIRKAADVHEVRKILGEKGKN-- 150 ::::::: ::::::::::::::::: d1rkda_ 164 -----PAPARELPDELLALVDIITP-NETEAEKLTGIRVENDEDAAKAAQVLHE----KG 213 d1a49a2 151 -IKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGRCNRAGKP 209 ::::::: d1rkda_ 214 IRTVLITL---------------------------------------------------- 221 d1a49a2 210 VICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAR 269 d1rkda_ 222 ------------------------------------------------------------ 222 d1a49a2 270 EAEAAMFHRKLFE----------------------------------------------- 282 d1rkda_ 222 -------------GSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALITALLEEKPL 268 d1a49a2 283 -------------------------------------- 283 d1rkda_ 269 PEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQR 306 TMalign alignment (TM-score: 0.37 Raw score:103.93) d1a49a2 1 ------------------------------------------IQTQQLHAAMADTFLEHM 18 d1rkda_ 1 AGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGA------------------ 42 d1a49a2 19 CRLDIDSAPITARNTGIICTIGPASRSVETLKEMIKSGMNVARMNFSH-----G--THEY 71 :::: ::: : :: ::::::::: : :::: d1rkda_ 43 ------------------NQAV-AAG----R--SG----ANIAFIACTGDDSIGESVRQQ 73 d1a49a2 72 HAE-TIKN----------------------------VRTATESFASDPILYRPVAVALDT 102 ::: :::: d1rkda_ 74 LATDNIDITPVSVIKGESTGVALIFVNGEGENVIGI------------------------ 109 d1a49a2 103 KG--PAVSEKDI-QDLKFGVEQ-DVDMVFASFIR-KAADVHEVRKILGEKGKNIKIISKI 157 :: :::::: ::::::::: ::::::::::: ::::::::: ::: :::::::::: d1rkda_ 110 HAGA--NAALSPALVEAQRERIANASALLMQLESP-LESVMAAAK-IAH-QNKTIVALNP 164 d1a49a2 158 E-NHEGVRRFDEILEASDGIMVARGDLGIEI--PAEKVFL--AQKMIIGRCNR-AGKPVI 211 : :::: : :::: :::::::::::::::: ::::: ::::::::::: :::::: d1rkda_ 165 APAREL--P-DELL-ALVDIITPNETEAEKLTG--IRVENDEDAAKAAQVLHEKGIRTVL 218 d1a49a2 212 CATQMLESMIKKPRPTRAEGSDVANA-----VLDG--------------------A---- 242 :: :: : ::: :: :::: : d1rkda_ 219 IT-LG-------------S-RGV-WASVNGEGQRVPGFRVQAVDTIAAGDTFNGALITAL 262 d1a49a2 243 -----D--CI--M--LS-GE-----TAKGDYP-LEAVRMQHLIAREAEAAMFHRKLFE 282 : :: : :: :: ::::::: :::::::::: : d1rkda_ 263 LEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQ--R------------ 306 HHsearch alignment (Probability: 0.61 E-value:0.01) d1a49a2 32 NTGIICTIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPI 91 :::::::::::::::::::::::::::::::::::::: ::::::::: :::: d1rkda_ 54 NIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGES-----TGVALIFVN-GEGE--- 104 d1a49a2 92 LYRPVAVAL-DTKGPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKILGEKGKN 150 ::::: ::::::::::::::::::: :::::::::::::::::::::::::::: d1rkda_ 105 ----NVIGIHAGANAALSPALVEAQRERI-ANASALLMQLESPLESVMAAAKIAHQNK-- 157 d1a49a2 151 IKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIP 188 :::::::::::::::::::::::::::::::::::: d1rkda_ 158 --TIVALNPAPARELPDELLALVDIITPNETEAEKLTG 193