HorA Server Transitive Detail

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


Query <-- 1.858 --> Intermediate <-- 1.188 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1t1ra2) through the intermediate protein (d1knwa2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1knwa2 Diaminopimelate decarboxylase LysAPLP-​binding barrelTIM beta/​alpha-​barrelα/β
Hit d1t1ra2 1-​deoxy-​D-​xylulose-​5-​phosphate reductoisomeraseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.858 --> Intermediate
DALI alignment (Z-score: 19.8 Raw score:1758.40) query 1 mietpyylidkaKLTRNMERIAHVRekSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::: ::::::::::::::::::::::::::::::::: d1knwa2 1 ------------DAQIIRRQIAALK--QFDVVRFAQKACSNIHILRLMREQGVKVDSVSL 46 query 61 FEVRLGRERFGK------ETHAYSVAYGDNEIDEVVSHaDKIIFNSISQLERFADKAAGI 114 :::::::::::: :::::::::::::::::::: ::::::::::::::::::::: d1knwa2 47 GEIERALAAGYNpqthpdDIVFTADVIDQATLERVSELqIPVNAGSVDMLDQLGQVSPGH 106 query 115 ARGLRLNPQ----------------RLGEW--DVPKVERVMD----RINGFMIHNNCeNK 152 ::::::::: ::::: :::::::::: ::::::::::: :: d1knwa2 107 RVWLRVNPGfghghsqktntggensKHGIWytDLPAALDVIQrhhlQLVGIHMHIGS-GV 165 query 153 DFGLFDRMLGEIEERFGALIARVDWVSLGGGIHF----tgDDYPVDAFSARLRAFSDRYG 208 :::::::::::::::::::::::::::::::::: :::::::::::::::::::: d1knwa2 166 DYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVpyqqgeEAVDTEHYYGLWNAAREQIA 225 query 209 ------VQIYLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakv 262 :::::::::::::: d1knwa2 226 rhlghpVKLEIEPGRFLVAQ---------------------------------------- 245 query 263 lpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpa 322 d1knwa2 246 ------------------------------------------------------------ 246 query 323 iaireldgsvrtvreftyadyeqsls 348 d1knwa2 246 ------------------------sg 247 FAST alignment (Normalized score: 11.38 Raw score:3336.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG--AKALLALKCFATWSVFDLMRDYM--DGTT 56 ::::::::::::: ::::::::::::::::::::: :::: d1knwa2 1 ---------DAQIIRRQIAALK-------QFDVVRFAQKACSNIHILRLMRE--QGVKVD 42 query 57 SSSLFEVRLGRERFGK-----------ETHAYSVAYGDNEIDEVVSHA--DKIIFNSISQ 103 ::::::::::: ::::::::::::::::::: :::::::::: d1knwa2 43 SVSLGEIERAL-----AAGYNPQTHPDDIVFTADVIDQATLERVSE--LQIPVNAGSVDM 95 query 104 LERFADKAAGIARGLRLNP-----------------QRLGEW---DVPKVERVMD----- 138 :::::::::::::::::: ::::: :::::::: d1knwa2 96 LDQLGQVSPGHRVWLRVN-PGFGHGHSQKTNTGGENSKHGI-WYTDLPAALDV--IQRHH 151 query 139 -RINGFMIHNNCE---NKDFGLFDRMLGEIEERFGALIA----RVDWVSLGGGIHFTGD- 189 :::::::: ::::::::::::::::::: :::::::::: d1knwa2 152 LQLVGIHMH----IGSGVDYAHLEQVCGAMVRQVI----EFGQDLQAISAGGG------L 197 query 190 ---------DYPVDAFSARLRAFSDRY-------GVQIYLEPGEASITKSTTLEVTVLDT 233 ::::::::::::::::: ::::::::::::::: d1knwa2 198 SVPYQQGEEAVDTEHYYGLWNAAREQ-IARHLGHPVKLEIEPGRFLVAQ----------- 245 query 234 LYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEEL 293 d1knwa2 246 ------------------------------------------------------------ 246 query 294 KVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-- 348 d1knwa2 246 -------------------------------------------------------SG 247 TMalign alignment (TM-score: 0.53 Raw score:185.85) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 :::::::::::: ::: : :::::::::::::::::::::::::::::: d1knwa2 1 ---------DAQIIRRQIAAL-KQF---D-VVRFAQKACSNIHILRLMREQGVKVDSVSL 46 query 61 FEVRLGRERFG----K--ETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGI 114 ::::::::::: : :::::::::::::::::::::::::::::::::::::::::: d1knwa2 47 GEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGH 106 query 115 ARGLRLNPQ----------------RLGE-WD-VPKVERVMD---RIN-GFMIHNNCENK 152 ::::::::: :::: :: ::::::::: ::: :::::::: :: d1knwa2 107 RVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGS-GV 165 query 153 DFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFT----GDDYPVDAFSARLRAFSDRYG 208 ::::::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1knwa2 166 DYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIA 225 query 209 ------VQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKV 262 :::::::::::::::: d1knwa2 226 RHLGHPVKLEIEPGRFLVAQSG-------------------------------------- 247 query 263 LPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPA 322 d1knwa2 248 ------------------------------------------------------------ 248 query 323 IAIRELDGSVRTVREFTYADYEQSLS 348 d1knwa2 248 -------------------------- 248 HHsearch alignment (Probability: 1.00 E-value:0.00) query 10 DKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRER 69 :::::::::::::::: ::::::::::::::::::::::::::::::::::::::: d1knwa2 1 DAQIIRRQIAALKQFD-----VVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAA 55 query 70 FGKET------HAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQ 123 ::::: ::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa2 56 GYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLRVNPG 115 query 124 ----------------RLGEWDVPKV------ERVMDRINGFMIHNNCENKDFGLFDRML 161 :::::::::: :::::::::::::::::: ::::::::: d1knwa2 116 FGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGV-DYAHLEQVC 174 query 162 GEIEERFGALIARVDWVSLGGGIHFTGDD----YPVDAFSARLRAFSDRY------GVQI 211 ::::::::::::::::::::::::::::: ::::::::::::::::: :::: d1knwa2 175 GAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHLGHPVKL 234 query 212 YLEPGEASITKST 224 ::::::::::::: d1knwa2 235 EIEPGRFLVAQSG 247
Intermediate <-- 1.188 --> Hit
DALI alignment (Z-score: 4.1 Raw score:349.60) d1knwa2 1 daqiirrqiaalkqfdvvrfaqkacsnihilrlmreqgvkvdsvslgeieralaagynpq 60 d1t1ra2 1 ------------------------------------------------------------ 1 d1knwa2 61 thpddivftadvidqatlervselqipvnagsvdmldqlgqvspgHRVWLR-VNPGfghg 119 :::::: :::: d1t1ra2 1 ---------------------------------------------KQLTILgSTGS---- 11 d1knwa2 120 hsqktntggenskhgIWYTDLPAALDVIQrhHLQLVGIHMHigsgvdyahleqVCGAMVR 179 :::::::::::::: :::::::::: ::::::: d1t1ra2 12 ---------------IGCSTLDVVRHNPE--HFRVVALVAG-----------kNVTRMVE 43 d1knwa2 180 QVIefGQDLQAISAGgglsvpyqqgeeavdtehYYGLWNAAREQIARHlGHPVKLEIEPG 239 ::: :::::::::: ::::::::::::::: ::::::::::: d1t1ra2 44 QCL--EFSPRYAVMD------------------DEASAKLLKTMLQQQ-GSRTEVLSGQQ 82 d1knwa2 240 -----------------------------------rflvaqsg 247 d1t1ra2 83 aacdmaaledvdqvmaaivgaagllptlaairagktillanke 125 FAST alignment (Normalized score: 2.58 Raw score:453.10) d1knwa2 1 DAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDSV------SLGEIERALA 54 :::::: :::::::::: d1t1ra2 1 --------------------------------------KQLTILGSTGSIGCSTLDVVRH 22 d1knwa2 55 AGYNPQTHPDD-------IVFTADVI--DQATLERVSELQI-PVNAGSVDMLDQLGQVS- 103 :::::: ::::::::::::: :::::::::::::::: d1t1ra2 23 -----------NPEHFRVVALVAG--KNVTRMVEQCLEFSPRYAVMDDEASAKLLKTM-L 68 d1knwa2 104 ----PGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHM 159 :::::: d1t1ra2 69 QQQGSRTEVL-------------------------------------------------- 78 d1knwa2 160 HIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNA 219 d1t1ra2 79 ------------------------------------------------------------ 79 d1knwa2 220 AREQIARHLGHPVKLEIEPGRFLVAQSG-------------------------------- 247 d1t1ra2 79 ----------------------------SGQQAACDMAALEDVDQVMAAIVGAAGLLPTL 110 d1knwa2 248 --------------- 248 d1t1ra2 111 AAIRAGKTILLANKE 125 TMalign alignment (TM-score: 0.29 Raw score:72.41) d1knwa2 1 DAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDSV-SLGEIERALAAG--Y 57 ::::::: :::::::::::: : d1t1ra2 1 -------------------------------------KQLTILGSTGSIGCSTLDVVRHN 23 d1knwa2 58 NP-QTHPDDIVFTADVIDQATLERVSEL-QI-PVNAGSVDMLDQLGQVSP----GHRVWL 110 :: :::: ::::::::: :::::::: :: :::::::::::::::::: :::::: d1t1ra2 24 PEH-FRVV--ALVAGKNVT-RMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLS 79 d1knwa2 111 RVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHL 170 ::: ::: d1t1ra2 80 GQQ-------------------------------------------AAC----------- 85 d1knwa2 171 EQVCGAM--VRQVIEFGQDLQAI-S-------------AGGGL-SVPYQQGEEAVDTEHY 213 : ::: : ::::: : d1t1ra2 86 ------DMA-----------ALEDVDQVMAAIVGAAGLLPTLAA---------------I 113 d1knwa2 214 YGLWNAAREQIARHLGHPVKLEIEPGRFLVA-QSG 247 : : :::::::: : d1t1ra2 114 R--A----------------GKTILLAN--KE--- 125 HHsearch alignment (Probability: 0.05 E-value:0.08) d1knwa2 151 HLQLVGIHMH 160 :::::::::: d1t1ra2 26 HFRVVALVAG 35