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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.714 --> Intermediate <-- 1.093 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1i6la_) through the intermediate protein (d1mopa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1mopa_ Pantothenate synthetase (Pantoate-​beta-​alanine ligase,​ PanC)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1i6la_ Tryptophanyl-​tRNA synthetase (TrpRS)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 0.714 --> Intermediate
DALI alignment (Z-score: 5.8 Raw score:745.80) query 1 -------dadeevysalvvglrayvaKNGFRSVLIGL-SGGI-DSALVAAIACDALgaqN 51 ::::::::::: :::: ::::::::::::: : d1mopa_ 1 ipafhpgelnvysapgdvadvsralrLTGRRVMLVPTmGALHeGHLALVRAAKRVP-gsV 59 query 52 VYGVSMPSK---------ysSDHSKGDAAELARRTGL-NFRTVSIEPMFDAYMA------ 95 ::::::::: ::::::::::::::::: :::::::::::::::: d1mopa_ 60 VVVSIFVNPmqfgaggdldaYPRTPDDDLAQLRAEGVeIAFTPTTAAMYPDGLRttvqpg 119 query 96 ----slgltgLAEENLQSRLRGTTLMAISNqeGHIVLAPGNkselavGYST--------l 143 :::::::::::::::::::: ::::::::: :::: d1mopa_ 120 plaaeleggpRPTHFAGVLTVVLKLLQIVR--PDRVFFGEK-----dYQQLvlirqlvad 172 query 144 ygdsvgAYGPiKDVY---kTSIFrlaewrnraaaergqtppipeaSITK-------pdYP 193 :::: :::: :::: :::: :: d1mopa_ 173 fnldvaVVGV-PTVReadgLAMS----------------------SRNRyldpaqraaAV 209 query 194 VLDAILELYvDRDT------GADAIVaAGYD---relvvKTLRmvDTAEYkrrqyppgtk 244 ::::::::: :::: :::::: :::: :::: ::::: d1mopa_ 210 ALSAALTAA-AHAAtagaqaALDAAR-AVLDaapgvavdYLEL--RDIGL---------- 255 query 245 isakgfgkdrrlpITNRWR-----------------------egh 266 :::::: d1mopa_ 256 ------------gPMPLNGsgrllvaarlgttrlldniaieigtf 288 FAST alignment (Normalized score: 3.14 Raw score:869.40) query 1 DADEEVYSALVVGLRAYVAKNGF------------------------------RSVLIGL 30 ::::::: d1mopa_ 1 -----------------------IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPT 37 query 31 S--GGIDSALVAAIACDALGAQ--NVYGVSMPS-----------KYSSDHSKGDAAELAR 75 : :::::::::::::::: :::::::: ::::: :::::::::: d1mopa_ 38 MGALHEGHLALVRAAKRVP---GSVVVVSIFV-NPMQFGAGGDLDAYPR-TPDDDLAQLR 92 query 76 RTGL-NFRTVSIEPM-FDAYMASLGL------------------TGLAEENLQSRLRGTT 115 :::: ::::: :::: :::::: :::::::::::::::: d1mopa_ 93 AEGVEIAFTP-TTAAMYPDGLR----TTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQI 147 query 116 LMAISNQEG---HIVLAPGNKSELAVGYSTLYGDSVG----------------------A 150 :::::: : d1mopa_ 148 ---------VRPDRVFFG-------------------EKDYQQLVLIRQLVADFNLDVAV 179 query 151 YGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP-------------------- 190 ::: d1mopa_ 180 VGV-------------------------------------PTVREADGLAMSSRNRYLDP 202 query 191 --------DYPVLDAILELYVDRDTGADAIVAAG-----YDRELVVKTLRMVDTAEYKRR 237 ::::::::: :::::::::::::: d1mopa_ 203 AQRAAAVALSAALTAAA-----------------HAATAGAQAALDAARAVLD------- 238 query 238 QYPPGTKISAKGFGKDRRLPITNRWREGH------------------------------- 266 d1mopa_ 239 -----------------------------AAPGVAVDYLELRDIGLGPMPLNGSGRLLVA 269 query 267 ------------------- 267 d1mopa_ 270 ARLGTTRLLDNIAIEIGTF 288 TMalign alignment (TM-score: 0.50 Raw score:134.27) query 1 ----------------------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSG 32 ::::::::::: d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLT---------------------GRRVMLVPTMG 39 query 33 -GI-DSALVAAIACDALGAQNVYGVSMPSK--------YS-SDHSKGDAAELARRTGL-N 80 :: :::::::::: ::::::::::::::: :: ::::::::::::::::: : d1mopa_ 40 ALHEGHLALVRAAK-RVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEI 98 query 81 FRTVSIEPMFDAYMASL-GL-----------TGLAEENLQSRLRGTTLMAISNQEGHIVL 128 ::::::::::::::::: : ::::::::::::::::::::: ::::: d1mopa_ 99 AFTPTTAAMYPDGLRTTV-QPGPLAAELEGG-PRPTHFAGVLTVVLKLLQIVR--PDRVF 154 query 129 APGNKSELAVGYSTLYGDSVG-----------AYGPIKDVYKTSIFRLAEWRNRAAAERG 177 :::: :: : : ::::: ::::: :::::::::: d1mopa_ 155 FGEK--DY--Q--Q--LVLIRQLVADFNLDVAVVGVP--TVREADGLAM----------- 193 query 178 QTPPIPEASITK-----P--DYPVLDAILELYVDRD-----TGADAIVAAGYDRE--LVV 223 ::::: : :::::::::::::::: :::::::: ::::: ::: d1mopa_ 194 -------SSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARA-VLDAAPGVAV 245 query 224 KTLRMVDTAEYKRR----------------------QYPPGTKISAKGFGKDRR--LPIT 259 ::: :::::::::: :::: :: d1mopa_ 246 DYL-ELRDIGLGPMPLNGSGRLLVAARLGTTRLLDN----------IAIE--IGTF---- 288 query 260 NRWREGH 266 d1mopa_ 289 ------- 289 HHsearch alignment (Probability: 0.01 E-value:0.62) query 53 YGVSMPSKYSSDHSKGDAAELARRT 77 ::::::::::::::::::::::::: d1mopa_ 191 LAMSSRNRYLDPAQRAAAVALSAAL 215
Intermediate <-- 1.093 --> Hit
DALI alignment (Z-score: 7.0 Raw score:847.70) d1mopa_ 1 ipafhpgelnvysapgdvadvsralrltgRRVMLVPTMG--ALHEGHLA-LVRAAKR-vp 56 :::::::::: :::::::: ::::::: d1i6la_ 1 -----------------------------MKTIFSGIQPsgVITIGNYIgALRQFVElqh 31 d1mopa_ 57 GSVVVVSIFVN-PMQFgaggDLDA---ypRTPDdDLAQLRAEGVEI----AFTP-TTAAM 107 ::::::::::: :::: :::: :::: :::::::::::: :::: ::::: d1i6la_ 32 EYNCYFCIVDQhAITV----WQDPhelrqNIRR-LAALYLAVGIDPtqatLFIQsEVPAH 86 d1mopa_ 108 YpdglRTTV------QPGPLA-aELEGG----PRPTHFAgVLTVVLKLLQIVRPDRVFFG 156 : :::: :::::: ::::: ::::::: :::::::::::::::::::: d1i6la_ 87 A-qaaWMLQcivyigELERMTqfKEKSAgkeaVSAGLLT-YPPLMAADILLYNTDIVPVG 144 d1mopa_ 157 EKdyqQLVLIRQLVADFN----------lDVAVVGV---PTVREAD--GLAMSSRNR--- 198 :: ::::::::::::: ::::::: ::::::: ::::::::: d1i6la_ 145 ED---QKQHIELTRDLAErfnkrygelftIPEARIPkvgARIMSLVdpTKKMSKSDPnpk 201 d1mopa_ 199 -------------yldpaqraaavalsaaLTAAA----------------------haat 223 ::::: d1i6la_ 202 ayitllddaktiekkiksavtdsegtiryDKEAKpgisnllniystlsgqsieelerqye 261 d1mopa_ 224 agaqaaldaaravldaapgvavdylelrdiglgpmplngsgrllvaarlgttrlldniai 283 d1i6la_ 262 gkgygvfkadlaqvvietlrpiqeryhhwmeseeldrvldegaekanrvasemvrkmeqa 321 d1mopa_ 284 eigtf 288 d1i6la_ 322 mglgr 326 FAST alignment (Normalized score: 4.99 Raw score:1529.00) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMG---ALHEGHL-ALVRAAK-RV 55 ::::::::: ::::::: ::::::: :: d1i6la_ 1 -----------------------------MKTIFSGIQ-PSGVITIGNYIGALRQFVELQ 30 d1mopa_ 56 PGSVVVVSIFVNPMQFGAGG---------DLDAYPR---TPDDDLAQLRAEGV----EIA 99 :::::::::: :::: :::::::::::::: ::: d1i6la_ 31 HEYNCYFCIV----------DQHAITVWQDPHE---LRQNIRRLAALYLAVGIDPTQATL 77 d1mopa_ 100 FTP--TTAAMYPDGLRTTVQP------------GPLAA-ELEGGP-----------RPTH 133 :: ::::: ::::: :::::: :::: d1i6la_ 78 FI-QSEVPAH-----------AQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTY 125 d1mopa_ 134 FAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNL----------DVAVVGV- 182 ::::::::::::::::::::::::::::::::::: ::::::: d1i6la_ 126 ----PPLMAADILLYNTDIVPVGEDQKQHIELTRDLAER---FNKRYGELFTIPEARIPK 178 d1mopa_ 183 --PTVREA--DGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLD 238 :::::: :::::::: d1i6la_ 179 VGARIMSLVDPTKKMSKS------------------------------------------ 196 d1mopa_ 239 AAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTF---------- 288 d1i6la_ 197 --------------------------------------------------DPNPKAYITL 206 d1mopa_ 289 ------------------------------------------------------------ 289 d1i6la_ 207 LDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYG 266 d1mopa_ 289 ------------------------------------------------------------ 289 d1i6la_ 267 VFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGR 326 TMalign alignment (TM-score: 0.47 Raw score:136.66) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGA--LHEGHLA-LVRAAKRV-P 56 : :::::::::: ::::::: :::::::: : d1i6la_ 1 ----------------------------M-KTIFSGIQPSGVITIGNYIGALRQFVELQH 31 d1mopa_ 57 GSVVVVSIFVNPMQFGAGGDLDA-YP-RTPDDDLAQLRA-EGVE---IAFTPTTAA-MYP 109 :::::::::::::::: :::: :: :::::::::::: :::: ::::::::: ::: d1i6la_ 32 EYNCYFCIVDQHAITV---WQDPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQ 88 d1mopa_ 110 DGLRTT--VQ-PG-PLAA-ELE-GGPR--P-THFAGVLTVVLKLLQIVRPDRVFFGEKDY 160 :::::: :: :: :::: ::: :::: : :::::::::::::::::::::::::: : d1i6la_ 89 AAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGE--D 146 d1mopa_ 161 QQLVLIRQLVADFN----------LDVAVVGV---PTVREAD-G-LAMSSRNRYLDPAQR 205 ::::::::::::: :::::::: ::::::: : ::::::: ::::::: d1i6la_ 147 -QKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSD-PNPKAYI 204 d1mopa_ 206 -----------A--AAVALSA------ALTAAAHAA------------------------ 222 : ::: :: ::::::: d1i6la_ 205 TLLDDAKTIEKKIK-SAV-TDSEGTIR--YDKEAKPGISNLLNIYSTLSGQSIEELERQY 260 d1mopa_ 223 ------------------------------------------------------------ 223 d1i6la_ 261 EGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQ 320 d1mopa_ 223 ------TAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTR 276 d1i6la_ 321 AMGLGR------------------------------------------------------ 326 d1mopa_ 277 LLDNIAIEIGTF 288 d1i6la_ 327 ------------ 327 HHsearch alignment (Probability: 0.56 E-value:0.00) d1mopa_ 32 VMLVPTMGALHEGHLA-LVRAAKRVPGSVVVVSIFVNP-MQFGAGGDLDAYPRTPDDDLA 89 :::::: ::::::::: ::::::::::::: ::::::: ::::::::::::::::::::: d1i6la_ 6 SGIQPS-GVITIGNYIGALRQFVELQHEYN-CYFCIVDQHAITVWQDPHELRQNIRRLAA 63 d1mopa_ 90 QLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLL---- 145 :::::::: ::::::::::: ::::::::::::::::::::::::::::::: d1i6la_ 64 LYLAVGID----PTQATLFIQSE--VPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEA 117 d1mopa_ 146 ----------------QIVRPDRVFFGEKDYQQLVLIRQLVADFNL-DVAVVGV--PTVR 186 :::::::::::::::::::::::::::::: ::::::: :::: d1i6la_ 118 VSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIP 177 d1mopa_ 187 EA--------DG-LAMSSR--N----RYLDPAQRAAAVALSAALTAAA 219 :: :: :::::: : :::::::::::::::::::::: d1i6la_ 178 KVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSE 225