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 <-- 2.312 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1a49a3) 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 d1a49a3 Pyruvate kinase,​ C-​terminal domainPK C-​terminal domain-​likePyruvate kinase C-​terminal domain-​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 <-- 2.312 --> Hit
DALI alignment (Z-score: 9.7 Raw score:719.60) d1t57a_ 1 mekkicyfeepgkENTERVLELVGERADQLGIRNFVVASVSGETALRLSEM-VEGNIVSV 59 :::::::::::::::::::::::::::::::::::::: :::::::: d1a49a3 1 ---elarssshstDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYrPRAPIIAV 57 d1t57a_ 60 THhagfrekgqlelEDEARDALLERG-VNVYAGSHalsgvgrgisnrfggvtpveimAET 118 :: :::::::::::: :::::::: ::: d1a49a3 58 TR------------NHQTARQAHLYRgIFPVVCKD--------------------pvQEA 85 d1t57a_ 119 LRmvsqgfkvcVEIAIMAAdaGLIP------VDEEVIAIGGT---AWGADTALVLTPAhm 169 :: :::::::: :::: ::::::::::: ::::::::::::: d1a49a3 86 WA------edvDLRVNLAM--NVGKargffkKGDVVIVLTGWrpgSGFTNTMRVVPVP-- 135 d1t57a_ 170 nsvfdlriheviamprp 186 d1a49a3 136 ----------------- 136 FAST alignment (Normalized score: 9.84 Raw score:1558.00) d1t57a_ 1 MEKKICYFEEPGK----------ENTERVLELVGERADQLGIRNFVVASVSGETALRLSE 50 ::::::::::::::::::::::::::::::::::::: d1a49a3 1 -------------ELARSSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVAR 47 d1t57a_ 51 -MVEGNIVSVTHHAGFREKGQLE-LEDEARDALLE-RGVNVYAGSHALSGVGRGISNRFG 107 ::::::::: ::::::::::: :::::: d1a49a3 48 YRPRAPIIAV-------------TRNHQTARQAHLYRGIFPV------------------ 76 d1t57a_ 108 GVTPVEIMAETLRMV-----------SQGFKVCVEIAIMAADAGLIPVDEEVIAIGGT-- 154 ::::::::::::::::::::::::::::::: d1a49a3 77 ---------------VCKDPVQEAWAEDVDLRVNLAMNVGKARGFFKKGDVVIVLTG-WR 120 d1t57a_ 155 --AWGADTALVLTPAHMNSVFDLRIHEVIAMPRP- 186 :::::::::::: d1a49a3 121 PGSGFTNTMRVVPV--------------------P 135 TMalign alignment (TM-score: 0.52 Raw score:96.63) d1t57a_ 1 ----------MEKKICYFEEPGKENTERVLELVGERADQLGIRNFVVASVSGETALRLSE 50 ::::::::::::::::::::::::::::::::::::: d1a49a3 1 ELARSSSHST-------------DLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVAR 47 d1t57a_ 51 M-VEGNIVSVTHHAGFREKGQLELEDEARDALLE-RGVNVYAG-SHALSGVGRGISNRFG 107 : :::::::::: ::: ::::::: :::::::: :: :: : d1a49a3 48 YRPRAPIIAVTR----------NHQ--TARQAHLYRGIFPVVCKDP-VQ---E------- 84 d1t57a_ 108 GVTPVEIMAETLRMVSQGFKVCVEIAIMAADA--GL-IPVD-EEVIAIGG-T-A-WGADT 160 :::: :: :::::::::: :: :::: :::::::: : : ::::: d1a49a3 85 -----AWAE----------DV-DLRVNLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNT 128 d1t57a_ 161 ALVLTPAHMNSVFDLRIHEVIAMPRP 186 ::::::: d1a49a3 129 MRVVPVP------------------- 135 HHsearch alignment (Probability: 0.90 E-value:0.00) d1t57a_ 11 PGKENTERVLELVGERADQLGIRNFVVASVSGETALRLSEMV-EGNIVSVTHHAGFREKG 69 :::::::::::::::::::::::::::::::::::::::::: :::::::::: d1a49a3 8 HSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRN------- 60 d1t57a_ 70 QLELEDEARDAL-LERGVNVYAGSHALSGVGRGISNRFGGVTPVEIMAET-LRMVSQGFK 127 ::::::: ::::::::::: :::::: ::::::::: d1a49a3 61 -----HQTARQAHLYRGIFPVVCK--------------------DPVQEAWAEDVDLRVN 95 d1t57a_ 128 VCVEIAIMAADAGLIPVDEEVIAIGGTAWGADTALV 163 :::: ::::::::::::::::::::::::::::: d1a49a3 96 LAMN---VGKARGFFKKGDVVIVLTGWRPGSGFTNT 128