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 <-- 2.347 --> Intermediate <-- 0.712 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1vk4a_) through the intermediate protein (d1tqja_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tqja_ D-​ribulose-​5-​phosphate 3-​epimeraseRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1vk4a_ Hypothetical protein TM0415Ribokinase-​likeRibokinase-​likeα/β

Supporting Alignments

Query <-- 2.347 --> Intermediate
DALI alignment (Z-score: 13.0 Raw score:1145.60) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCF---aTWSVFDLMRD-YMDGTT 56 ::::::::::: :::::::::: :::::: d1tqja_ 1 ---------------------------kNIVVAPSILSAdfsrLGEEIKAVDEaGADWIH 33 query 57 SSS------------LFEVRLGRERFGKETHAYSV--AYGDnEIDEVVS-HADKIIFNS- 100 ::: :::::::::::::::::::: :::: ::::::: ::::::::: d1tqja_ 34 VDVmdgrfvpnitigPLIVDAIRPLTKKTLDVHLMivEPEK-YVEDFAKaGADIISVHVe 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDRINGFMIHN-NCENkdf 154 :::::::::::: ::::::::::: :::::::::::::::::::: :::: d1tqja_ 93 hnaSPHLHRTLCQIRelGKKAGAVLNPS----TPLDFLEYVLPVCDLILIMSvNPQS--- 145 query 155 glFDRMLGEIEeRFGALIA---RVDWVSLGGGIHFtgddypvdaFSARLRAFSdrygvqI 211 ::::::::: ::::::: ::::::::::::: ::::::::: : d1tqja_ 146 -fIPEVLPKIR-ALRQMCDergLDPWIEVDGGLKP--------nNTWQVLEAG-----aN 190 query 212 YLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsy 271 ::::::::::: d1tqja_ 191 AIVAGSAVFNA------------------------------------------------- 201 query 272 micgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgs 331 d1tqja_ 202 ------------------------------------------------------------ 202 query 332 vrtvreftyadyeqsls 348 d1tqja_ 202 --pnyaeaiagvrnskr 216 FAST alignment (Normalized score: 7.32 Raw score:2007.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALK-CFA--TWSVFDLMRD-YMDGT 55 ::::::::: ::: :::::::::: ::::: d1tqja_ 1 ----------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWI 32 query 56 TS------------SSLFEVRLGRERFGKETHAYSVAY----GDNEIDEVVS-HADKIIF 98 :: ::::::::::::::::::::: :::::::::: ::::::: d1tqja_ 33 HVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHL---MIVEPEKYVEDFAKAGADIISV 89 query 99 N--SISQ---LERFADKA---AGIARGLRLNPQRLGE-WDVPKVERVMDRINGFMIHNNC 149 :::: ::::::: ::::::::::: :::::::::::::::::::: d1tqja_ 90 -HVEHNASPHLHRTLCQ-IRELGKKAGAVLNP-----STPLDFLEYVLPVCDLILIMS-- 140 query 150 ENKD------FGLFDRMLGEIEERFGALIARV----DWVSLGGGIHFTGDDYPVDA---F 196 ::::::::::::::::: ::::::::: : d1tqja_ 141 ----VNPQSFIPEVLPKIRALRQMCDE-----RGLDPWIEVDGGL-----------KPNN 180 query 197 SARLRAFSDRYGVQ---IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::: ::::::::: d1tqja_ 181 TWQVLE--------AGANAIVAGSAV---------------------------------- 198 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 d1tqja_ 199 ------------------------------------------------------------ 199 query 314 WFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------------------ 348 d1tqja_ 199 -----------------------------------FNAPNYAEAIAGVRNSKR 216 TMalign alignment (TM-score: 0.43 Raw score:149.23) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF-A--TWSVFDLMRD-YMDGTT 56 :::::::::::: : :::::::::: :::::: d1tqja_ 1 ---------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWIH 33 query 57 S-S-----------SLFEVRLGRERFGKETHAYSVA--YGDNEIDEVVS-HADKIIFNS- 100 : : :::::::::::::::::::::: ::: ::::::: ::::::::: d1tqja_ 34 VDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPEK-YVEDFAKAGADIISVHVE 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNN--CENKD 153 :::::::::::: ::::::::::: :::: ::::::::::::::::: ::: d1tqja_ 93 HNASPHLHRTLCQIRELGKKAGAVLNPS---TPLD-FLEYVLPVCDLILIMSVNPQSF-- 146 query 154 FGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQ 210 : ::::::::::::::: ::::::::::::: ::: :: :: ::: : d1tqja_ 147 ---I-PEVLPKIRALRQMCDERGLDPWIEVDGGLKP----NNT--WQ-VL-EAG-----A 189 query 211 IYLEPGEASITKST-------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYR 257 :::::::::::::: d1tqja_ 190 NAIVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 query 258 ETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNG 317 d1tqja_ 217 ------------------------------------------------------------ 217 query 318 VKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1tqja_ 217 ------------------------------- 217 HHsearch alignment (Probability: 0.21 E-value:0.01) query 75 HAYSVAYGDNEIDEVVSHADKIIFN--SISQLERFADKAAG--IARGLRLNPQRLGEWDV 130 ::::::::::::::::::::::::: :::::::::::::: :::::::::: ::: d1tqja_ 68 MIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPS----TPL 123 query 131 PKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDW-VSLG 181 ::::::::::::::::::::::::::::::::::::::::::::::: :::: d1tqja_ 124 DFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175
Intermediate <-- 0.712 --> Hit
DALI alignment (Z-score: 3.7 Raw score:503.80) d1tqja_ 1 ---knivVAPSIL------------------------------------SADF------- 14 :::::: :::: d1vk4a_ 1 ihhhhhhMITFIGhvskdvnvvdgkreiaygggvvmgaitssllgvktkVITKctredvs 60 d1tqja_ 15 -----------------------------------------sRLGEEIkavdeagADWIH 33 :::::: ::::: d1vk4a_ 61 kfsflrdngvevvflksprttsienrytresflisaadpfteSDLAFI------eGEAVH 114 d1tqja_ 34 VDVMDgrfvpNITIGPLIVDAIRPLTkKTLDVHLM-----------ivepeKYVEDFAKa 82 ::::: :::::::::::::::: :::::::: :::::::: d1vk4a_ 115 INPLW-----YGEFPEDLIPVLRRKV-MFLSADAQgfvrvpeneklvyrdwEMKEKYLK- 167 d1tqja_ 83 GADIISVHVehNASP------HLHRTLCQIRELGK-KAGAVLnpstpLDFL----eYVLP 131 ::::::::: :::: :::::::::::::: :::::: :::: :::: d1vk4a_ 168 YLDLFKVDS--REAEtltgtnDLRESCRIIRSFGAkIILATH-----ASGVivfdgNFYE 220 d1tqja_ 132 vcdlilimsvnpqsfIPEV-------lpkiralrqmcdergLDPW--IEVD---gglkpn 179 :::: :::: :::: d1vk4a_ 221 --------asfrswsLEGRtgrgdtctaaflvgfvfkkmsiEKATkfAAAVtsvkmrhpg 272 d1tqja_ 180 NTWQ-vLEAGanaivagsavfnapnyaeaiagvrnskr 216 :::: :::: d1vk4a_ 273 PLRRedLEAI---------------------------s 283 FAST alignment (Normalized score: 2.04 Raw score:503.40) d1tqja_ 1 KNIVVAPSILSADFSRLGEEIKA------------------------------------- 23 d1vk4a_ 1 -----------------------IHHHHHHMITFIGHVSKDVNVVDGKREIAYGGGVVMG 37 d1tqja_ 24 ---VDEAGADWIHVDVMDGRF--------------------------------------- 41 ::::::::::: d1vk4a_ 38 AITSSLLGVKTKVI-------TKCTREDVSKFSFLRDNGVEVVFLKSPRTTSIENRYTRE 90 d1tqja_ 42 --VPNI--TIGPLIVDAIRPLTK----KTLDVHLMIVEPEKYVEDFAKAGADIISVHVEH 93 :::: :::::::: :::::::::: d1vk4a_ 91 SFLISAADPFTESDLA-------FIEGEAVHINPLWY----------------------- 120 d1tqja_ 94 NASPHL----HRTLCQIRELG--KKAGAVLNP--------------STPLDFLEYVLPVC 133 ::::::::: :::::: :::::::::::::: d1vk4a_ 121 ------GEFPEDLIPVLRR--KVMFLSAD---AQGFVRVPENEKLVYRDWEMKEKYLKYL 169 d1tqja_ 134 DLILIMSVNPQSFI----------PEVLPKIRALRQMCDERGLD---PWIEVDGGLKPNN 180 :::::: :::::::::::: ::::::: d1vk4a_ 170 DLFKVD--------SREAETLTGTNDLRESCRIIRS--------FGAKIILATH------ 207 d1tqja_ 181 TWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRNSKR------------------------ 216 d1vk4a_ 208 ------------------------------------ASGVIVFDGNFYEASFRSWSLEGR 231 d1tqja_ 217 ---------------------------------------------------- 217 d1vk4a_ 232 TGRGDTCTAAFLVGFVFKKMSIEKATKFAAAVTSVKMRHPGPLRREDLEAIS 283 TMalign alignment (TM-score: 0.48 Raw score:103.93) d1tqja_ 1 ------KNIVVAPSIL------------------------------------SA------ 12 ::::::: :: d1vk4a_ 1 IHHHHH---HMITFIGHVSKDVNVVDGKREIAYGGGVVMGAITSSLLGVKTKVITKCTRE 57 d1tqja_ 13 -----------------D------------------------FS-RLGEEIKAVDEAGAD 30 : :: :::::: :: : d1vk4a_ 58 DVSKFSFLRDNGVEVVFLKSPRTTSIENRYTRESFLISAADPFTESDLAFI--EG----E 111 d1tqja_ 31 WIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLM--I---------VEPEKYVEDF 79 ::::::::: ::::::::::::::: :::::::: : :::::::::: d1vk4a_ 112 AVHINPLWY-----GEFPEDLIPVLRRKV-MFLSADAQGFVRVPENEKLVYRDWEMKEKY 165 d1tqja_ 80 AKAGADIISVHVEHNAS-----PHLHRTLCQIRE-LGKKAGAVLNPSTPLDFLEYVLP-- 131 :: :::::::::: ::: :::::::::::: ::::::::: ::: : ::: d1vk4a_ 166 LK-YLDLFKVDSR-EAETLTGTNDLRESCRIIRSFGAKIILATH----ASG-V--IVFDG 216 d1tqja_ 132 VCDLI-LI-MS--VNPQSFIPEVL-PK--IR---ALR----------QMCDERGLDPW-- 169 ::::: : : ::::: : :: : ::::: d1vk4a_ 217 NFYEAS-FR-SWS------LEGRTG-RGDTCTAA--FLVGFVFKKMS------IEKATKF 259 d1tqja_ 170 IE-VD--G----GLKPNNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRNSKR 216 :: :: : ::: ::::::::: d1vk4a_ 260 AAAVTSVKMRHPGPL--RREDLEAIS---------------------------- 283 HHsearch alignment (Probability: 0.28 E-value:0.09) d1tqja_ 22 KAVDEAGADWIHVDVMDGRF 41 :::::::::::::::::::: d1vk4a_ 63 SFLRDNGVEVVFLKSPRTTS 82