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 <-- 1.647 --> Intermediate <-- 1.043 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1k6wa2) through the intermediate protein (d1d3ga_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1d3ga_ Dihydroorotate dehydrogenaseFMN-​linked oxidoreductasesTIM beta/​alpha-​barrelα/β
Hit d1k6wa2 Cytosine deaminase catalytic domainMetallo-​dependent hydrolasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.647 --> Intermediate
DALI alignment (Z-score: 7.2 Raw score:865.90) query 1 mietpyyLIDKAK-----------------------------------ltrnmeriahvr 25 :::::: d1d3ga_ 1 -------MATGDErfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevrvlg 53 query 26 eksgaKALLALKcfatwsvfDLMRD-YMDGTTSSSL------------------------ 60 ::::::: ::::: :::::::::: d1d3ga_ 54 hkfrnPVGIAAGfdkhgeavDGLYKmGFGFVEIGSVtpkpqegnprprvfrlpedqavin 113 query 61 ----------------fevrlgRERFG---KETHAYSVA---------YGDNEIDEVVSH 92 ::::: ::::::::: :::::::::::: d1d3ga_ 114 rygfnshglsvvehrlrarqqkQAKLTedgLPLGVNLGKnktsvdaaeDYAEGVRVLGPL 173 query 93 ADKIIFNS-------------ISQLERFADKAA------GIARGLRLNPQrlgewDVPKV 133 :::::::: :::::::::::: ::::::::::: ::::: d1d3ga_ 174 ADYLVVNVsspntaglgkaelRRLLTKVLQERDglrrvhRPAVLVKIAPD-ltsqDKEDI 232 query 134 ERVM--DRINGFMIHNN-------------------CENKdfglFDRMLGEIEErFGALI 172 :::: ::::::::::: :::: :::::::::: ::::: d1d3ga_ 233 ASVVkeLGIDGLIVTNTtvsrpaglqgalrsetgglSGKP---lRDLSTQTIREmYALTQ 289 query 173 ARVdWVSLGGGIHFtgddypvdAFSARLRAFSdrygvqIYLEPGEASITKSttlevtvld 232 ::: :::::::::: :::::::::: ::::::::::::: d1d3ga_ 290 GRV-PIIGVGGVSS-------gQDALEKIRAG-----aSLVQLYTALTFWG--------- 327 query 233 tlynknlaivdssieahmldlliyretakvlpnegshsymicgksclagdvfgefrfaee 292 d1d3ga_ 328 ------------------------------------------------------------ 328 query 293 lkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1d3ga_ 328 -----------------------ppvvgkvkreleallkeqgfggvtdaigadhrr 360 FAST alignment (Normalized score: 4.17 Raw score:1474.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA------------------------------ 30 d1d3ga_ 1 ------------------------------MATGDERFYAEHLMPTLQGLLDPESAHRLA 30 query 31 ----------------------------KALLALKCFA--TWSVFDLMR-DYMDGTTSS- 58 :::::::: ::::::::: ::::::: d1d3ga_ 31 VRFTSLGLLPFQDSDMLEVRVLGHKFRNPVGIAAGF--DKHGEAVDGLYKMGFGFVE--I 86 query 59 -----------------------------------SLFEVRLGRERFG------------ 71 :::::::::: d1d3ga_ 87 GSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRA---RQQKQAKLTEDG 143 query 72 KETHAYSVAY------------GDNEIDEVVSHADKIIFN--------------SISQLE 105 ::::::: ::::::::::::::::: :::::: d1d3ga_ 144 LPLGVNL---GKNKTSVDAAEDYAEGVRVLGPLADYLVV-NVSSPNTAGLGKAELRRLLT 199 query 106 RFADKAA------GIARGLRLNPQRLGEW---------DVPKVERVMD-RINGFMIHNNC 149 ::::::: :::::::::: ::::::: :::::: d1d3ga_ 200 KVLQERDGLRRVHRPAVLVKIAP------DLTSQDKEDIASVVKE---LGIDGLI----- 245 query 150 ENK---------------------------DFGLFDRMLGEIEERFGALIARV----DWV 178 ::::::::::::::: ::: d1d3ga_ 246 ---VTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYAL--------TQGRVPI 294 query 179 SLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQ--IYLEPGEASITKSTTLEVTVLDTLY 235 :::::: ::::::::::: ::::::::: d1d3ga_ 295 IGVGGV-----------SSGQDALEKIRA----GASLVQLYTAL---------------- 323 query 236 NKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKV 295 d1d3ga_ 324 ------------------------------------------------------------ 324 query 296 GDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------- 348 d1d3ga_ 324 -----------------------------------------------------TFWGPPV 330 query 349 ------------------------------ 349 d1d3ga_ 331 VGKVKRELEALLKEQGFGGVTDAIGADHRR 360 TMalign alignment (TM-score: 0.36 Raw score:123.76) query 1 ---------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWS-------- 43 :: d1d3ga_ 1 MATGDERFY-----------------------------------------AEHLMPTLQG 19 query 44 -------VFDLMRDYMDGTTSSSLFE--VR----L-GRE---------------RFGKET 74 ::::: : : :: :::: d1d3ga_ 20 LLDPESA--------------HRLAVRF-TSLGLLP-FQDSDMLEVRVLGHKFR--NPVG 61 query 75 HAY--SVAYGDNEIDEVVSH-A-DKIIF-N------------------------------ 99 ::: ::::: :::::::: : ::::: : d1d3ga_ 62 IAAGFDKHGE--AVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNS 119 query 100 --SISQLERFA-D--KAA-G----IARGLRLNPQR-L--G-EWDVPKVERVMDRINGFMI 145 ::::::::: : ::: : ::::::::::: : : ::::::::::::::::::: d1d3ga_ 120 HGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVV 179 query 146 HNNCEN---KDFGLFDRMLGEIEERFGALIA------RVDWVSLGGGIHFTGDDYPVDAF 196 :::::: :::::::::::::::::: ::::::::: ::: ::: :: d1d3ga_ 180 NVSSPNTAG----LGKAELRRLLTKVLQERDGLRRVHRPAVLVKIA-PDL----TSQ-DK 229 query 197 SARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIY 256 :::::::::::::::::::::: ::::::: :::::: : d1d3ga_ 230 EDIASVVKELGIDGLIVTNTTV-SRPAGLQ---------------------GALRSE--T 265 query 257 RETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV------ 310 : :::::: d1d3ga_ 266 -G----------------------------------------------GLSGKPLRDLST 278 query 311 ------------------------------------------------------------ 311 d1d3ga_ 279 QTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKREL 338 query 311 ----------------------KKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1d3ga_ 339 EALLKEQGFGGVTDAIGADHRR-------------------------------------- 360 HHsearch alignment (Probability: 0.13 E-value:0.02) query 98 FNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDR-INGFMI----------- 145 :::::::::::::::::::::::::::::::::::::::::: :::::: d1d3ga_ 198 LTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGL 257 query 146 -----HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGG 182 ::::::::::::::::::::::::::::::::::::: d1d3ga_ 258 QGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGG 299
Intermediate <-- 1.043 --> Hit
DALI alignment (Z-score: 7.9 Raw score:971.30) d1d3ga_ 1 matgderfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevrvlghkfRNPV 60 :::: d1k6wa2 1 --------------------------------------------------------PFVE 4 d1d3ga_ 61 GIAaGFDK---------------------------------hgEAVDGLYKMG-----fG 82 ::: :::: :::::::::: : d1k6wa2 5 PHI-HLDTtqtagqpnwnqsgtlfegierwaerkallthddvkQRAWQTLKWQiangiqH 63 d1d3ga_ 83 FVEIGSVTPKPqegnprprvfrlpedqavinrygfnshglSVVEHRLRARQQKQAKLTed 142 ::::::::::: :::::::::::::::::: d1k6wa2 64 VRTHVDVSDAT-----------------------------LTALKAMLEVKQEVAPWI-- 92 d1d3ga_ 143 gLPLGV-NLGKnktsvDAAEDyAEGVRVLGP-LADYLVVNVSSpntagLGKAELRRLLTK 200 ::::: :::: ::::: ::::::::: ::::::::::: :::::::::::: d1k6wa2 93 -DLQIVaFPQE--gilSYPNG-EALLEEALRlGADVVGAIPHF----eFTREYGVESLHK 144 d1d3ga_ 201 VLQERDGLrrvhRPAVLVKI-APDLtSQDKedIASVVKELG-------iDGLIVtnttvs 252 :::::::: :::::::: :::: :::: ::::::::: ::::: d1k6wa2 145 TFALAQKY----DRLIDVHCdEIDD-EQSR--FVETVAALAhhegmgarVTASH------ 191 d1d3ga_ 253 rpaglqgalrsetgglsgkplrdlstqTIRE--------myALTQ-gRVPIIGVGGV--- 300 :::: :::: :::::::::: d1k6wa2 192 -------------------------ttAMHSyngaytsrlfRLLKmsGINFVANPLVnih 226 d1d3ga_ 301 -------ssgqdaleKIRAG-----aSLVQL-YTAL--TFWGPPVVgKVKRELEA--lLK 343 ::::: ::::: :::: :::::::: :::::::: :: d1k6wa2 227 lqgrfdtypkrrgitRVKEMlesginVCFGHdDVFDpwYPLGTANMlQVLHMGLHvcqLM 286 d1d3ga_ 344 EQGF--GGVT---------------daigadhrr 360 :::: :::: d1k6wa2 287 GYGQinDGLNlithhsartlnlqdygiaagnsan 320 FAST alignment (Normalized score: 4.41 Raw score:1496.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNP- 59 d1k6wa2 1 -----------------------------------------------------------P 1 d1d3ga_ 60 VGIAAGFDKHG---------------------------------------------EAVD 74 :::: :::: d1k6wa2 2 FVEP-------HIHLDTTQTAGQPNWNQSGTLFEGIERWAERKALLTHDDVKQRAWQTLK 54 d1d3ga_ 75 GLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSH------GLSVVEHR 128 ::::::::::: ::::: :::::::: d1k6wa2 55 WQIANGIQHVR-THVDV-----------------------------SDATLTALKAMLEV 84 d1d3ga_ 129 LRARQQKQAKLTEDG-LPLGVNLGKNKT------SVDAAEDYAEGVRVLGPLADYLVVNV 181 :::::: ::::::::: ::::::::::::: :::::::::: d1k6wa2 85 KQEVAP---------WIDLQIVAFP---QEGILSYPNGEALLEEALR---LGADVVGAIP 129 d1d3ga_ 182 SSPNTAG---LGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTS---------QDK 229 ::::::::::::::::::: :::::::: ::: d1k6wa2 130 -------HFEFTREYGVESLHKTFALAQK----YDRLIDVH-------CDEIDDEQSRFV 171 d1d3ga_ 230 EDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLS------------ 277 ::::::::::: d1k6wa2 172 ETVAALAHHEG-------------------------------------MGARVTASHTTA 194 d1d3ga_ 278 -----TQTIREMYALTQ---GRVPIIGVGGVSSGQ----------------------DAL 307 :::::::::: ::::::: ::: d1k6wa2 195 MHSYNGAYTSRLFRL--LKMSGINFVA--------NPLVNIHLQGRFDTYPKRRGITRVK 244 d1d3ga_ 308 EKIRAGA----SLVQLYTALTFWGPP--------------VVGKVKRELEALLKEQGFGG 349 :::: :::: :::::::::::: d1k6wa2 245 EMLE---SGINVCFG-----------HDDVFDPWYPLGTANMLQVLHMGLHV-------- 282 d1d3ga_ 350 VTDAIGADHRR-------------------------------------- 360 d1k6wa2 283 -----------CQLMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSAN 320 TMalign alignment (TM-score: 0.48 Raw score:173.62) d1d3ga_ 1 ------------MATGDERFYAEHLMPTLQG----LLDPESAHRLAVRFTSLGL--LP-- 40 ::: ::::::: :::::::::::::::::: :: d1k6wa2 1 PFVEPHIHLDTT-------QTA--GQPNWNQSGTL-FEGIERWAERKALLTHDDVKQRAW 50 d1d3ga_ 41 ---FQ-DSDMLEVRVLGHKFRNPVGIAAGFDKHG--E-AVDGLY-KM--G---F-GFVE- 85 :: :::::: :: :: : ::::: : :::::: :: : : :::: d1k6wa2 51 QTLKWQIANGIQ--------HV--RT-H-VDVSDATLTALKAMLEVKQEVAPWIDLQIVA 98 d1d3ga_ 86 IGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLP 145 ::::::::: :::::::::::: :: : : d1k6wa2 99 FPQEGILSY------------------------PNGEALLEEALR-LG--A--------D 123 d1d3ga_ 146 LGVNLGK-NKTSVDAAEDYAEGVRVLG-PLADYLVVNVSSPNTAGLGKAELRRLLTKVLQ 203 ::::::: ::::::::::::::::::: ::::::::: ::::::::: ::::::::::: d1k6wa2 124 VVGAIPHFEFTREYGVESLHKTFALAQKYDRLIDVHC-DEIDDEQSR--FVETVAALAHH 180 d1d3ga_ 204 ERDGLRRVHRPAVLVK-I-A-PDLTSQDKEDIASVVKELGIDGLIVT---N--TTV-SRP 254 ::: ::::::: : : ::::::::::::::::::: :::::: : ::: ::: d1k6wa2 181 EGM------GARVTASHTTAMHSYNGAYTSRLFRLLKMSG-INFVANPLVNIHLQGRFDT 233 d1d3ga_ 255 AGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGA 314 :: :: ::: :::::::: :: ::: : d1k6wa2 234 YP---------------KR-RGI-TRVKEMLE-SG--INV-------------------C 254 d1d3ga_ 315 SLVQLYTALTFWGPPVVGKVKRELE-AL--------------LKEQGFGGVTDAIGA--- 356 :::::::::::: :: ::::::: : ::::::: d1k6wa2 255 -FGHDDVFDPWYP--LG-TANMLQVL-HMGLHVCQLMGYGQI--------NDGLNLITHH 301 d1d3ga_ 357 -------------------DHRR 360 d1k6wa2 302 SARTLNLQDYGIAAGNSAN---- 320 HHsearch alignment (Probability: 0.01 E-value:1.70) d1d3ga_ 297 VGGVSSGQDALEKIR-AGASLVQLYTA 322 ::::::::::::::: ::::::::::: d1k6wa2 285 LMGYGQINDGLNLITHHSARTLNLQDY 311