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_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.802 --> Intermediate <-- 1.276 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1pfka_) through the intermediate protein (d1jfla2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jfla2 Aspartate racemaseAspartate/​glutamate racemaseATC-​likeα/β
Hit d1pfka_ ATP-​dependent phosphofructokinasePhosphofructokinasePhosphofructokinaseα/β

Supporting Alignments

Query <-- 0.802 --> Intermediate
DALI alignment (Z-score: 1.0 Raw score:191.90) query 1 slqLRLALNQ-------------------------------IDST------VGDIAGNAE 23 ::::::: :::: ::::::::: d1jfla2 1 --fKKAGLLAttgtivsgvyekefskygveimtptedeqkdVMRGiyegvkAGNLKLGRE 58 query 24 AILRWTRHSAEQGAHLVAF-PEMAltgypvedlalrssfveasrtalrelAARLaeegfg 82 ::::::::::::::::::: :::: :::: d1jfla2 59 LLLKTAKILEERGAECIIAgCTEV----------------------svvlKQDD-----l 91 query 83 ELPVLvgyldrsesaqpkygqpagaprnaaavlhrgrvaltfakhhlpnygvfdefryfv 142 ::::: d1jfla2 92 KVPLI------------------------------------------------------- 96 query 143 pgdtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlel 202 d1jfla2 97 ------------------------------------------------------------ 97 query 203 vrkraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaa 262 d1jfla2 97 ------------------------------------------------------------ 97 query 263 eaepptgvvddglridrlviseeplpayeaelaggyadrl 302 d1jfla2 97 -----------------------dpmdviaevavkvalek 113 FAST alignment (Normalized score: 1.26 Raw score:232.10) query 1 SLQLRLALNQIDSTVGDIAGNAEAI---------------LRWTRHSAEQGAHLVAFPEM 45 :::::::::::: d1jfla2 1 -------------------------FKKAGLLATTGTIVSGVYEKEFSKYGV-------- 27 query 46 ALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPA 105 d1jfla2 28 ------------------------------------------------------------ 28 query 106 GAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDL 165 d1jfla2 28 ------------------------------------------------------------ 28 query 166 WQDG----------------------------------GRVPAARSAGAGLLLSVNASPY 191 :::::::::::::::: d1jfla2 28 ----EIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIA------ 77 query 192 ERDKD--DTRLELVRK-RAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQF 248 :::::: ::::::::::: d1jfla2 78 -----GCTEVSVV---LKQDDLKVPLID-------------------------------- 97 query 249 SEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL------ 302 d1jfla2 98 ------------------------------------------------------PMDVIA 103 query 303 ---------- 303 d1jfla2 104 EVAVKVALEK 113 TMalign alignment (TM-score: 0.20 Raw score:60.72) query 1 -SLQLR-LA-LN-QIDSTV-GDIAGN--AEAI--LRWT-RHSAEQGAHLV-AF-----PE 44 : : : :::: : : :: :: :::::: : d1jfla2 1 F----KK-AG-LL--ATTGT-----IVS---GVY--EKE-FS--KYGVEIM-TPTEDE-- 36 query 45 MA-LTG-YPV---EDLALRSSFVEASRTALRELAARLAEEGFGELPVLVG-Y--LDRSES 96 : ::: ::: :: :::::::::::::::::::: : : ::::: : :: d1jfla2 37 -QKDVMRGIYEGVKA-GNLKLGRELLLKTAKILEER-G----A--ECIIAGCTEVS---- 83 query 97 AQPKYGQPAGAPRNAAA--VLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHG 154 ::::: :::::::: d1jfla2 84 ------------VVLKQDD-----LKVPLIDP---------------------------- 98 query 155 VDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTT 214 :::: : : : : :::::: d1jfla2 99 ----MDVI--A------E----------V-------------------A--VKVALE--- 112 query 215 AYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDG 274 : d1jfla2 113 -----------------------K------------------------------------ 113 query 275 LRIDRLVISEEPLPAYEAELAGGYADRL 302 d1jfla2 114 ---------------------------- 114 HHsearch alignment (Probability: 0.06 E-value:0.03) query 16 GDIAGNAEAILRWTRHSAEQGAHLVAF 42 ::::::::::::::::::::::::::: d1jfla2 51 GNLKLGRELLLKTAKILEERGAECIIA 77
Intermediate <-- 1.276 --> Hit
DALI alignment (Z-score: 4.3 Raw score:372.00) d1jfla2 1 -FKKAGLLA----ttGTIVS-GVYEKEFSKYGVEIMTPtedeQKDVM------------- 41 :::::::: ::::: ::::::::::::::::: ::::: d1pfka_ 1 mIKKIGVLTsggdapGMNAAiRGVVRSALTEGLEVMGI----YDGYLglyedrmvqldry 56 d1jfla2 42 -------------rgIYEGvkagnlkLGRE--lllKTAKILEERGAECIIAGCT-EVSVV 85 :::: :::: ::::::::::::::::::: ::::: d1pfka_ 57 svsdminrggtflgsARFP-------EFRDeniraVAIENLKKRGIDALVVIGGdGSYMG 109 d1jfla2 86 LK--QDDLkVPLIDPM-------------------------------------------- 99 :: :::: ::::::: d1pfka_ 110 AMrlTEMG-FPCIGLPgtidndikgtdytigfftalstvveaidrlrdtssshqrisvve 168 d1jfla2 100 ------------------------------------------------------------ 100 d1pfka_ 169 vmgrycgdltlaaaiaggcefvvvpevefsredlvneikagiakgkkhaivaitehmcdv 228 d1jfla2 100 -------------------------------------------------------DVIAe 104 :::: d1pfka_ 229 delahfieketgretratvlghiqrggspvpydrilasrmgayaidlllagyggrCVGI- 287 d1jfla2 105 vAVKV-------------------------alek 113 :::: d1pfka_ 288 -QNEQlvhhdiidaienmkrpfkgdwldcakkly 320 FAST alignment (Normalized score: 1.01 Raw score:191.60) d1jfla2 1 FKKAGLLATTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEG------------- 47 d1pfka_ 1 -----------------------------------------------MIKKIGVLTSGGD 13 d1jfla2 48 ------------------------------------------------------------ 48 d1pfka_ 14 APGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSAR 73 d1jfla2 48 ------------------------------------------------------------ 48 d1pfka_ 74 FPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKG 133 d1jfla2 48 ----------------------------------------------------------VK 49 :: d1pfka_ 134 TDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFVVVP 193 d1jfla2 50 AGNLKL-GRELLLKTAKILEERGAECIIAGCTEVSVVLKQDDLKVPLID----------- 97 ::: :::::::::::::::::::::: d1pfka_ 194 EVE---FSREDLVNEIKAGIAKGKKHAIV--------------------AITEHMCDVDE 230 d1jfla2 98 --------------------------------PMDVIAEVAVKVALEK------------ 113 :::::::::::::: d1pfka_ 231 LAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLL--LAGYGGRCVGIQ 288 d1jfla2 114 -------------------------------- 114 d1pfka_ 289 NEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY 320 TMalign alignment (TM-score: 0.57 Raw score:63.92) d1jfla2 1 -FKKAGLLAT--T---GTIVSGVYEKEFSKYGVEIMTPTEDEQK--DV------------ 40 ::::::::: : :::::::::::::::::::::: :: :: d1pfka_ 1 MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGI----YDGYLGLYEDRMVQLDRY 56 d1jfla2 41 --------------MRGIYEGVKAGNLKLGREL--LLKTAK-ILEERGAECIIAGCT-EV 82 ::: : :: ::: :::::: ::::::::::::::: :: d1pfka_ 57 SVSDMINRGGTFLGSAR---F------PE-FRDENIRAVAIENLKKRGIDALVVIGGDGS 106 d1jfla2 83 SVVL-K-QDDLKVPLIDPM----------------------------------------- 99 :::: : ::: :::::::: d1pfka_ 107 YMGAMRLTEM-GFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRIS 165 d1jfla2 100 ------------------------------------------------------------ 100 d1pfka_ 166 VVEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHM 225 d1jfla2 100 ----------------------------------------------------------DV 101 :: d1pfka_ 226 CDVDELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCV 285 d1jfla2 102 IAE--VAVK--------------------------VALEK 113 ::: :::: d1pfka_ 286 GIQNEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY----- 320 HHsearch alignment (Probability: 0.02 E-value:0.15) d1jfla2 55 LGRELLLKTAKILEERGAECIIAGCTEVSV---------------VLKQDDLKVPLIDPM 99 :::::::::::::::::::::::::::::: ::::::::::::::: d1pfka_ 78 RDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKGTDYT 137