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 <-- 1.067 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1ir6a_) 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 d1ir6a_ Exonuclease RecJDHH phosphoesterasesDHH phosphoesterasesα/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 <-- 1.067 --> Hit
DALI alignment (Z-score: 4.4 Raw score:411.10) d1l7da1 1 ----agyraviDGAYEFaRAFPMmmtaagtvppARVLVFG-----vGVAGLQAIATAKRL 51 :::::: ::::: ::::::: :::::::::::::: d1ir6a_ 1 plallplkglrEAAALLeEALRQ---------gKRIRVHGdydadgLTGTAILVRGLAAL 51 d1l7da1 52 GAVVMATDVRAAtkeqveslggkfitvkkQAEAVLKELVKTDIAITTAlipgkpaPVLIT 111 :::::::::::: ::::::::::::::::::: ::::: d1ir6a_ 52 GADVHPFIPHRL-----------eegygvLMERVPEHLEASDLFLTVD-----cgITNHA 95 d1l7da1 112 -EEMVTKMKpgSVIIDLAVEAGgncplsepgkivvkhgvkIVGHTN-------------- 156 :::::::: ::::::::::: :::::: d1ir6a_ 96 eLRELLENG--VEVIVTDHHTP------------gktpppGLVVHPaltpdlkekptgag 141 d1l7da1 157 ------------------------------------------------------------ 157 d1ir6a_ 142 vaflllwalherlglpppleyadlaavgtiadvaplwgwnralvkeglaripasswvglr 201 d1l7da1 157 ------------------------------------------------------------ 157 d1ir6a_ 202 llaeavgytgkavevafriaprinaasrlgeaekalrllltddaaeaqalvgelhrlnar 261 d1l7da1 157 ------------------------------------------------------------ 157 d1ir6a_ 262 rqtleeamlrkllpqadpeakaivlldpeghpgvmgivasrileatlrpvflvaqgkgtv 321 d1l7da1 157 ------------------------------------------------------------ 157 d1ir6a_ 322 rslapisavealrsaedlllrygghkeaagfamdealfpafkarveayaarfpdpvreva 381 d1l7da1 157 vpsr 160 d1ir6a_ 382 lldl 385 FAST alignment (Normalized score: 2.79 Raw score:692.50) d1l7da1 1 A------------GYRAVIDGAYEFARAFPMMMTAAGTVP-PARVLVFGV--------GV 39 :::::::::: :::::: :: d1ir6a_ 1 -PLALLPLKGLREAAALLEEALR-----------------QGKRIRV---HGDYDADGLT 39 d1l7da1 40 AGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVK------------KQAEAVLK 87 :::::::::::::::::::: :::::::: d1ir6a_ 40 GTAILVRGLAALGADVHPFI--------------------PHRLEEGYGVLMERVPEHLE 79 d1l7da1 88 ELVKTDIAITTALIPGKPAPVLI---------TEEMVTKMKPGSVIIDLAVEAGGNCPLS 138 ::::::: ::::::: ::::::: d1ir6a_ 80 ---ASDLFLT-------------VDCGITNHAELRELLE--NGVEVIV------------ 109 d1l7da1 139 EPGKIVVKHGVK------------IVGHTNVPSR-------------------------- 160 :::: d1ir6a_ 110 ------------TDHHTPGKTPPPGLVV------HPALTPDLKEKPTGAGVAFLLLWALH 151 d1l7da1 161 ------------------------------------------------------------ 161 d1ir6a_ 152 ERLGLPPPLEYADLAAVGTIADVAPLWGWNRALVKEGLARIPASSWVGLRLLAEAVGYTG 211 d1l7da1 161 ------------------------------------------------------------ 161 d1ir6a_ 212 KAVEVAFRIAPRINAASRLGEAEKALRLLLTDDAAEAQALVGELHRLNARRQTLEEAMLR 271 d1l7da1 161 ------------------------------------------------------------ 161 d1ir6a_ 272 KLLPQADPEAKAIVLLDPEGHPGVMGIVASRILEATLRPVFLVAQGKGTVRSLAPISAVE 331 d1l7da1 161 ------------------------------------------------------ 161 d1ir6a_ 332 ALRSAEDLLLRYGGHKEAAGFAMDEALFPAFKARVEAYAARFPDPVREVALLDL 385 TMalign alignment (TM-score: 0.50 Raw score:79.60) d1l7da1 1 ---A--GYR-AVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-----GVAGLQAIATAK 49 : : :::::::::::::: :::::::::: :::::::::::: d1ir6a_ 1 PLALLP--LKGLREAAALLEEALR---------QGKRIRVHGDYDADGLTGTAILVRGLA 49 d1l7da1 50 RLGAVVMATDVRA--------ATKEQVESLGGKFITVKKQAEAVLKELVKTDIAITTALI 101 ::::::::::::: ::::::::::: : ::::::: d1ir6a_ 50 ALGADVHPFIPHRLEEGYGVL----------------MERVPEHLEAS--D-LFLTVDC- 89 d1l7da1 102 PGKPAPVLITEEMVTKMKPGSVIIDLAVEAGG--NCPLSEPGKIVVKHGVKIVGHT---- 155 ::::::::::::::: :::::::::::: :::: ::::: d1ir6a_ 90 ---GITNHAELRELLENG--VEVIVTDHHTPGKT-PPPG------------LVVHPALTP 131 d1l7da1 156 ----NV---PS--R---------------------------------------------- 160 :: :: : d1ir6a_ 132 DLKEKPTGAGVAFLLLWALHERLGLPPPLEYADLAAVGTIADVAPLWGWNRALVKEGLAR 191 d1l7da1 161 ------------------------------------------------------------ 161 d1ir6a_ 192 IPASSWVGLRLLAEAVGYTGKAVEVAFRIAPRINAASRLGEAEKALRLLLTDDAAEAQAL 251 d1l7da1 161 ------------------------------------------------------------ 161 d1ir6a_ 252 VGELHRLNARRQTLEEAMLRKLLPQADPEAKAIVLLDPEGHPGVMGIVASRILEATLRPV 311 d1l7da1 161 ------------------------------------------------------------ 161 d1ir6a_ 312 FLVAQGKGTVRSLAPISAVEALRSAEDLLLRYGGHKEAAGFAMDEALFPAFKARVEAYAA 371 d1l7da1 161 -------------- 161 d1ir6a_ 372 RFPDPVREVALLDL 385 HHsearch alignment (Probability: 0.02 E-value:0.31) d1l7da1 28 PPARVLVFG---VGV--AGLQAIATAKRLGAVVMATDV---------RAATKEQVESLGG 73 ::::::::: ::: ::::::::::::::::::::: ::::::::::::: d1ir6a_ 23 QGKRIRVHGDYDADGLTGTAILVRGLAALGADVHPFIPHRLEEGYGVLMERVPEHLEASD 82 d1l7da1 74 KFITV 78 ::::: d1ir6a_ 83 LFLTV 87