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 <-- 0.826 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1vi9a_) 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 d1vi9a_ Pyridoxamine kinaseRibokinase-​likeRibokinase-​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 <-- 0.826 --> Hit
DALI alignment (Z-score: 4.0 Raw score:310.70) d1l7da1 1 agyravidgayefarafpmmmtaagtvPPARVLVFGVG-----VAGLQAIATAKRLGAVV 55 ::::::::::: ::::::::::::::::: d1vi9a_ 1 ---------------------------LMKNILAIQSHvvyghAGNSAAEFPMRRLGANV 33 d1l7da1 56 MATD-VRAAtkeqveslggkfitvkkqAEAVLKE-----LVKTDIAITTALIpgkPAPV- 108 :::: :::: ::::::: ::::::::::::: :::: d1vi9a_ 34 WPLNtVQFSnhtqygkwtgxvmppshlTEIVQGIaaidkLHTCDAVLSGYLG--sAEQGe 91 d1l7da1 109 LITEeMVTKM---KPGSVII---------------------------------------- 125 :::: ::::: ::::::: d1vi9a_ 92 HILG-IVRQVkaaNPQAKYFcdpvmghpekgcivapgvaefhvrhglpasdiiapnlvel 150 d1l7da1 126 ------------------------------------------------------------ 126 d1vi9a_ 151 eilcehavnnveeavlaareliaqgpqivlvkhlaragysrdrfemllvtadeawhisrp 210 d1l7da1 126 -------------------------------------------dlaveaggncplsepgk 142 d1vi9a_ 211 lvdfgmrqpvgvgdvtsglllvkllqgatlqealehvtaavyeimvttkamqeyelqvva 270 d1l7da1 143 ivvkhgvkivghtnvpsr 160 d1vi9a_ 271 aqdriakpehyfsatkle 288 FAST alignment (Normalized score: 2.92 Raw score:627.20) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVG--------VAGLQAIATAKRLG 52 :::::::: :::::::::::::: d1vi9a_ 1 ---------------------------LMKNILAI---QSHVVYGHAGNSAAEFPMRRLG 30 d1l7da1 53 AVVMATDVRAATKEQVESLGGKFITV------------------KKQAEAVL-------- 86 ::::::::: ::::: d1vi9a_ 31 ANVWPLNTV-----------------QFSNHTQYGKWTGAVMPPSHLTE---IVQGIAAI 70 d1l7da1 87 KELVKTDIAITTALIPGKPAPVLI-----------TEEMVTK---MKPGSVIIDLAVEAG 132 ::::::::::: ::::::: ::::::::: d1vi9a_ 71 DKLHTCDAVLS-------------GYLGSAEQGEHILGIVRQVKAANPQAKYFC------ 111 d1l7da1 133 GNCPLSEPGKIVVKHGVK-----------------------------IVGHTNVPSR--- 160 :::: d1vi9a_ 112 ------------------DPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIA------PNL 147 d1l7da1 161 ------------------------------------------------------------ 161 d1vi9a_ 148 VELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHI 207 d1l7da1 161 ------------------------------------------------------------ 161 d1vi9a_ 208 SRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQ 267 d1l7da1 161 --------------------- 161 d1vi9a_ 268 VVAAQDRIAKPEHYFSATKLE 288 TMalign alignment (TM-score: 0.39 Raw score:61.73) d1l7da1 1 ----------------AGY---RAVI--DGA----YEFARAFP----------------- 18 :: :: : :::: d1vi9a_ 1 LMKNILAIQSHVVYGH-AGNSA--AEFP--MRRLG----ANVWPLNTVQFSNHTQYGKWT 51 d1l7da1 19 ------------M--MM-TAAGT-VPPARVLVF-------------------------GV 37 : :: ::::: ::::::::: d1vi9a_ 52 GAVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKY-- 109 d1l7da1 38 GVAGLQAIATAKRLGAVVMATD----VRAATKEQVESLGGKFITVKKQAEAVLKELVKTD 93 ::::::: :: :::: ::: : ::::::::::: d1vi9a_ 110 ---------------FCDPVMGHPEKGC-IVAP--------GVA---E-FHVRHGLPASD 141 d1l7da1 94 IAITTALIPGKPAPVL-I------------T-EEMVTKMKPGSVIIDLAVEAGG------ 133 ::::::: :::: : : ::::::::: ::::::::::: d1vi9a_ 142 IIAPNLV-----ELEILCEHAVNNVEEAVLAARELIAQGPQ--IVLVKHLARAGYSRDRF 194 d1l7da1 134 NCPLSEPGKIVVKHGVKIVGHTN------------------------------------- 156 :::::::: ::::::: d1vi9a_ 195 ------EMLLVTAD--EAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEH 246 d1l7da1 157 -V--PSR----------------------------------- 160 : ::: d1vi9a_ 247 VTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKLE 288 HHsearch alignment (Probability: 0.04 E-value:0.06) d1l7da1 37 VGVAGLQAI-ATAKRLGAVVMAT 58 ::::::::: ::::::::::::: d1vi9a_ 14 YGHAGNSAAEFPMRRLGANVWPL 36