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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.100 --> Intermediate <-- 0.933 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1tuga1) through the intermediate protein (d1l7da1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1l7da1 Nicotinamide nucleotide transhydrogenase dI componentNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1tuga1 Aspartate carbamoyltransferase catalytic subunitAspartate/​ornithine carbamoyltransferaseATC-​likeα/β

Supporting Alignments

Query <-- 1.100 --> Intermediate
DALI alignment (Z-score: 5.1 Raw score:345.40) query 1 ---------------GMEN----------KKMNLLLfsgdydkALASLIIANAAREMEIE 35 :::: ::::::: ::::::::::::::::: d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFG------vGVAGLQAIATAKRLGAV 54 query 36 VTIFCafwgLLLLrdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllem 95 ::::: :::: d1l7da1 55 VMATD----VRAA----------------------------------------------- 63 query 96 mkeekapklsdllSGARKKEVKFYAXQLsveimgfkkeelfpevqimDVKEYLKNALESD 155 ::::::::::::::: ::::::::::::: d1l7da1 64 -----------tkEQVESLGGKFITVKK-------------------QAEAVLKELVKTD 93 query 156 LQLFI------------------------------------------------------- 160 ::::: d1l7da1 94 IAITTalipgkpapvliteemvtkmkpgsviidlaveaggncplsepgkivvkhgvkivg 153 query 161 ------- 161 d1l7da1 154 htnvpsr 160 FAST alignment (Normalized score: 3.90 Raw score:624.80) query 1 GME----------------------------NKKMNLLLFSGDYDK---ALASLIIANAA 29 :::::: ::::::::::: d1l7da1 1 ---AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLV---------FGVGVAGLQAIATA 48 query 30 REMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGK 89 :::::::::: d1l7da1 49 KRLGAVVMAT-------------------------------------------------- 58 query 90 KMLLEMMKEEKAPKLSD-----LLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-- 142 :::::::::::::: d1l7da1 59 -----------------DVRAATKEQVESLGGKFIT----------------------VK 79 query 143 -DVKEYLKNALESDLQLFI----------------------------------------- 160 :::::::::::::::: d1l7da1 80 KQAEAVLKELVKTDIAI--TTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPL 137 query 161 ----------------------- 161 d1l7da1 138 SEPGKIVVKHGVKIVGHTNVPSR 160 TMalign alignment (TM-score: 0.23 Raw score:37.44) query 1 ------------------------------GMENKKMNLLLFSGDYDKALASLIIANAAR 30 d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPA------------------------------ 30 query 31 EMEIEVTIFCAFWGLLLLRDPEK--AS--QEDKSLYEQAFSSLTPREAE----------- 75 :: ::: ::::: :: :::::: : :: :: ::: d1l7da1 31 -----------RV-LVF-GVGVAGLQAIATAKRLG-A--VV--MA-TDVRAATKEQVESL 71 query 76 ---ELPL-SK-----------------MNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK 114 :::: :: ::::::: d1l7da1 72 GGKFITVKKQAEAVLKELVKTDIAITT--------------------------ALIPGKP 105 query 115 EVKFYA---X----QLSVEIMGFKKEELFPE---V----Q----IMDVKEY--------- 147 :::::: : :::: : : :::: : : ::::::: d1l7da1 106 APVLITEEMVTKMKPGSV----I-I--DLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVP 158 query 148 --LKNALESDLQLFI 160 d1l7da1 159 SR------------- 160 HHsearch alignment (Probability: 0.09 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1l7da1 40 AGLQAIATAKRLGAVVMAT 58
Intermediate <-- 0.933 --> Hit
DALI alignment (Z-score: 10.4 Raw score:747.40) d1l7da1 1 ------------------------------------------------------------ 1 d1tuga1 1 anplyqkhiisindlsrddlnlvlataaklkanpqpellkhkviascffaastrtrlsfe 60 d1l7da1 1 ------------------------------------------------------------ 1 d1tuga1 61 tsmhrlgasvvgfsdsantslgkkgetladtisvistyvdaivmrhpqegaarlatefsg 120 d1l7da1 1 ----------------AGYRAVIDGAYEFaRAFPmmmtaagtvpPARVLVFG---vGVAG 41 ::::::::::::: :::: :::::::: :::: d1tuga1 121 nvpvlnagdgsnqhptQTLLDLFTIQETQ-GRLD----------NLHVAMVGdlkyGRTV 169 d1l7da1 42 LQAIATAKRL-GAVVMATDVR-AATKEQVESLG------GKFITvkkqaeAVLKELVKTD 93 :::::::::: :::::::::: ::::::::::: ::::: :::::::::: d1tuga1 170 HSLTQALAKFdGNRFYFIAPDaLAMPQYILDMLdekgiaWSLHS------SIEEVMAEVD 223 d1l7da1 94 IAITTALIPGK---------papvLITEEMVTKMKPGSVIIDLAvEAGGNCPLsepgkiV 144 ::::::::::: :::::::::::::::::::: :::::::: : d1tuga1 224 ILYMTRVQKERldpseyanvkaqfVLRASDLHNAKANMKVLHPL-PRVDEIAT----dvD 278 d1l7da1 145 VKHgvKIVGH--TNVPSR---------------- 160 ::: ::::: :::::: d1tuga1 279 KTP--HAWYFqqAGNGIFarqallalvlnrdlvl 310 FAST alignment (Normalized score: 5.18 Raw score:1154.00) d1l7da1 1 ------------------------------------------------------------ 1 d1tuga1 1 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFAASTRTRLSFE 60 d1l7da1 1 ------------------------------------------------------------ 1 d1tuga1 61 TSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSG 120 d1l7da1 1 ----------------AGYRAVIDGAYEFARAFPMMMTAAGTVP----PARVLVFGV--- 37 ::::::::::::: ::::::: d1tuga1 121 NVPVLNAGDGSNQHPTQTLLDLFTIQETQ---------------GRLDNLHVAMV--GDL 163 d1l7da1 38 --GVAGLQAIATAKRL-GAVVMATD-----VRAATKEQVESL--GGKFITVKKQAE--AV 85 :::::::::::::: :::::::: :::::::::::: :::: :: d1tuga1 164 KYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSL--------HSSI 215 d1l7da1 86 LKELVKTDIAITTALIPGKPAPV--------------------LITEEMVTKMKPGSVII 125 :::::::::::: ::::::::::::::::: d1tuga1 216 EEVMAEVDILYM-----------TRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVL 264 d1l7da1 126 DLAVEAGGNCPLSEPGKIV------------VKHGVKIVG------HTNVPSR------- 160 : :::: :::::: d1tuga1 265 H------------------PLPRVDEIATDVDKTP-----HAWYFQQAGNGI-FARQALL 300 d1l7da1 161 ---------- 161 d1tuga1 301 ALVLNRDLVL 310 TMalign alignment (TM-score: 0.65 Raw score:104.32) d1l7da1 1 ------------------------------------------------------------ 1 d1tuga1 1 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFAASTRTRLSFE 60 d1l7da1 1 ------------------------------------------------------------ 1 d1tuga1 61 TSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSG 120 d1l7da1 1 ----------------AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVF-GV--GVAG 41 ::::::::::::: :::: ::::::: :: :::: d1tuga1 121 NVPVLNAGDGSNQHPTQTLLDLFTIQETQ-GRLD----------NLHVAMVGDLKYGRTV 169 d1l7da1 42 LQAIATAKRLG-AVVMATDV-RAATKEQVESLG----G-KFITVKKQAEAVLKELVKTDI 94 ::::::::::: :::::::: :::::::::::: : :::: :: :::::::::: d1tuga1 170 HSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLH---SS--IEEVMAEVDI 224 d1l7da1 95 AITTALIPG----------KPAP--VLITEEMVTKMKPGSVIIDLAVEAGGNCP--LSEP 140 ::::::::: : ::::::::::::::::::::: ::::::: :: d1tuga1 225 LYMTRVQKERLDPSEYANV---KAQFVLRASDLHNAKANMKVLHPL-PRVDEIATDVD-- 278 d1l7da1 141 GKIVVKHGVKIVG-HTNVPS--R-------------- 160 : : :::::: :::::: : d1tuga1 279 ---K-T-PHAWYFQQAGNGIFARQALLALVLNRDLVL 310 HHsearch alignment (Probability: 0.96 E-value:0.00) d1l7da1 24 AGTVPPARVLVFGV---GVAGLQAIATAKRL-GAVVMATD-----VRAATKEQVESLGGK 74 :::::::::::::: :::::::::::::: :::::::: ::::::::::::::: d1tuga1 149 QGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIA 208 d1l7da1 75 FITVKKQAEAVLKELVKTDIAITTALIP---------GKPAPVLITEEMVTKMKPGSVII 125 ::: ::::::::::::::::::::: ::::::::::::::::::::::: d1tuga1 209 WSL----HSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVL 264 d1l7da1 126 D 126 : d1tuga1 265 H 265