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 <-- 0.668 --> Intermediate <-- 0.693 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1hnja1) through the intermediate protein (d1t57a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1t57a_ Hypothetical protein MTH1675PK C-​terminal domain-​likePyruvate kinase C-​terminal domain-​likeα/β
Hit d1hnja1 Ketoacyl-​ACP synthase III (FabH)Thiolase-​likeThiolase-​likeα/β

Supporting Alignments

Query <-- 0.668 --> Intermediate
DALI alignment (Z-score: 4.8 Raw score:501.90) query 1 ---------dadeeVYSALVVGLRAYVAKNGFRSVLIGLSGgidsALVAAIACDALGaQN 51 ::::::::::::::::::::::::::: :::::::::::: :: d1t57a_ 1 mekkicyfeepgkeNTERVLELVGERADQLGIRNFVVASVS----GETALRLSEMVE-GN 55 query 52 VYGVSMPSK---YSSDhSKGD-AAELARRTGLNFRTVSI--ePMFDAYMASLGLtglaEE 105 ::::::::: :::: :::: ::::::::::::::::: :::::::::::: :: d1t57a_ 56 IVSVTHHAGfreKGQL-ELEDeARDALLERGVNVYAGSHalsGVGRGISNRFGG---vTP 111 query 106 NL----------qsrlrgTTLMAISNQ-------eGHIVLAPGnkselavgystlygdsV 148 :: ::::::::: :::::::: : d1t57a_ 112 VEimaetlrmvsqgfkvcVEIAIMAADaglipvdeEVIAIGGT-----------awgadT 160 query 149 GAYgpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtg 208 ::: d1t57a_ 161 ALV--------------------------------------------------------- 163 query 209 adaivaagydrelvvktlrmvdtaeykrrqyPPGTkisakgfgkdrrlpitnrwregh 266 :::: d1t57a_ 164 ----------------ltpahmnsvfdlrihEVIA-------------------mprp 186 FAST alignment (Normalized score: 3.32 Raw score:738.10) query 1 DAD------------EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDS--ALVAAIACDA 46 ::::::::::::::::::::::::::: :::::::::: d1t57a_ 1 ---MEKKICYFEEPGKENTERVLELVGERADQLGIRNFVVAS------VSGETALRLSEM 51 query 47 LGAQ--NVYGVSMPSKYSSDH-------------SKGDAAELARRTGLNFRTVSI----- 86 : :::::: ::::::::: ::::::::: d1t57a_ 52 V---EGNIVSVT---------HHAGFREKGQLELEDEARDALL-ERGVNVYAG--SHALS 96 query 87 EPMFDAYMASLGLTGLAEENLQ-----------------------SRLRGTTLMAI---- 119 ::::::::: :::::::::: d1t57a_ 97 GVGRGISNR-------------FGGVTPVEIMAETLRMVSQGFKVCVEIAIMAAD-AGLI 142 query 120 SNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQT 179 :::::::::: d1t57a_ 143 PVDEEVIAIG-------------------------------------------------- 152 query 180 PPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQY 239 d1t57a_ 153 ------------------------------------------------------------ 153 query 240 PPGTKISAKGFGKDRRLPITNRWREGH--------------------------------- 266 d1t57a_ 153 ---------------------------GTAWGADTALVLTPAHMNSVFDLRIHEVIAMPR 185 query 267 - 267 d1t57a_ 186 P 186 TMalign alignment (TM-score: 0.36 Raw score:96.37) query 1 ---------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACD 45 :::::::::::::::::::::::::: :: ::::::: d1t57a_ 1 MEKKICYFEEPGKEN------TERVLELVGERADQLGIRNFVVASVS---GE-TALRLSE 50 query 46 ALGAQNVYGVSMPSKYSS--DHSKGD-AAELARRTGLNFRTVSIEPMFDAYMASL-GLTG 101 ::: :::::::::::::: :::::: :::::::::::::::::::::::::::: ::: d1t57a_ 51 MVE-GNIVSVTHHAGFREKGQLELEDEARDALLERGVNVYAGSHALSGVGRGISNRFGG- 108 query 102 LAE--ENL--QSRL---------RG-TTLMA--I----SNQE-GHIVLAPGNKSELAVGY 140 :: : :: :: ::::: : :::: :::::::: d1t57a_ 109 -VTPV--EIM--AETLRMVSQGFKVCVEIAIMAADAGLIPVDEEVIAIGGT--------- 154 query 141 STLYGDSVGAY----------------GPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPE 184 ::: :::::: d1t57a_ 155 -AWG-ADTALVLTPAHMNSVFDLRIHE--------------------------------- 179 query 185 ASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTK 244 :::: d1t57a_ 180 ------------------------------------------------------VIAM-- 183 query 245 ISAKGFGKDRRLPITNRWREGH 266 : : : d1t57a_ 184 -----P-R-----P-------- 186 HHsearch alignment (Probability: 0.08 E-value:0.04) query 16 AYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELAR 75 :::::::::::::::::: :::::::::: ::::::::::::::::::::::::::: d1t57a_ 25 ERADQLGIRNFVVASVSG----ETALRLSEMV-EGNIVSVTHHAGFREKGQLELEDEARD 79 query 76 RT 77 :: d1t57a_ 80 AL 81
Intermediate <-- 0.693 --> Hit
DALI alignment (Z-score: 3.5 Raw score:331.90) d1t57a_ 1 -----mekkiCYFEE------------------------------pgKENT-ERVLELVG 24 ::::: :::: :::::::: d1hnja1 1 mytkiigtgsYLPEQvrtnadlekmvdtsdewivtrtgirerhiaapNETVsTMGFEAAT 60 d1t57a_ 25 ERADQL-----GIRNFVVASV-----sGETALRLSEMV---EGNIVSVThhagfrekgql 71 :::::: :::::::::: ::::::::::: :::::::: d1hnja1 61 RAIEMAgiekdQIGLIVVATTsathafPSAACQIQSMLgikGCPAFDVA----------- 109 d1t57a_ 72 eledeardallergvnvyagshalsgvgrgisnrfggvtpveimaetlrmvsqgfKVCVE 131 ::::: d1hnja1 110 ----------------------------------------------------aacAGFTY 117 d1t57a_ 132 IAIMAADaglIPVD---EEVIAIGGTAW----------------gaDTALVLTpahmnsV 172 ::::::: :::: ::::::::::: ::::::: : d1hnja1 118 ALSVADQ---YVKSgavKYALVVGSDVLartcdptdrgtiiifgdgAGAAVLA---aseE 171 d1t57a_ 173 FDLriheviamprp 186 ::: d1hnja1 172 PGI----------- 174 FAST alignment (Normalized score: 3.37 Raw score:606.80) d1t57a_ 1 MEKK---------ICYFEEPGK------------------------------------EN 15 :::: :: d1hnja1 1 ----MYTKIIGTGSYLP-----EQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETV 51 d1t57a_ 16 TERVLELVGERADQL-----GIRNFVVASVSG-------ETALRLSEMVE---GNIVSVT 60 ::::::::::::::: :::::::::: ::::::::::: :::::: d1hnja1 52 STMGFEAATRAIEMAGIEKDQIGLIVVATT--SATHAFPSAACQIQSMLGIKGCPAFDV- 108 d1t57a_ 61 HHAGFREKGQLELEDEARDALLERGVNVYAGSHALSGVGRGISNRFGGVTPVEIMAETLR 120 d1hnja1 109 ------------------------------------------------------------ 109 d1t57a_ 121 MV---SQGFKVCVEIAIMAADAGLIPVD-EEVIAIGGTAWGA------------------ 158 ::::::::::::::::::: ::::::: d1hnja1 109 --AAACAGFTYALSVADQYVKSGA----VKYALVVG------SDVLARTCDPTDRGTIII 156 d1t57a_ 159 ----DTALVLTPAHMNSVFDLRIHEVIAMPRP-------- 186 :::::: d1hnja1 157 FGDGAGAAVL----------------------AASEEPGI 174 TMalign alignment (TM-score: 0.39 Raw score:71.84) d1t57a_ 1 -------MEKKICYF----------------------------EEPG---KENTERVLEL 22 :::::: :::: :::::::::: d1hnja1 1 MYTKIIG--TGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEA 58 d1t57a_ 23 VGERADQ-LGI--RN-FVVAS------VSGETALRLSEMV-EGNIVSVTHHAGFREKGQL 71 ::::::: ::: :: ::::: ::::::::::::: ::::::::: : d1hnja1 59 ATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDV---A------ 109 d1t57a_ 72 ELEDEARDALLERGVNVYAGSHALSGVGRGISNRFGGVTPVEIMAETLRMVSQGFKVCVE 131 : : ::::::::: d1hnja1 110 ---------------------A--------------------------A--CAGFTYALS 120 d1t57a_ 132 IAIMAADAGLIPVDEEVIAIGGTAW-----------------GADTALVLTPAHMNSVFD 174 :::::::::::: :::::::::: :::::::::: : :: d1hnja1 121 VADQYVKSGAVK---YALVVGSDVLARTCDPTDRGTIIIFGD-GAGAAVLAAS---E-EP 172 d1t57a_ 175 LRIHEVIAMPRP 186 :: d1hnja1 173 GI---------- 174 HHsearch alignment (Probability: 0.02 E-value:0.11) d1t57a_ 30 LGIRNFVVAS 39 :::::::::: d1hnja1 37 TGIRERHIAA 46