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 <-- 1.905 --> Intermediate <-- 2.197 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1dv1a2) through the intermediate protein (d1vl2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1dv1a2 Biotin carboxylase (BC),​ N-​terminal domainPreATP-​grasp domainPreATP-​grasp domainα/β

Supporting Alignments

Query <-- 1.905 --> Intermediate
DALI alignment (Z-score: 12.5 Raw score:953.20) query 1 dadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 ySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK----DV 157 :::::::::::::: :::::::: :::: :::: :::::: :: d1vl2a1 95 IAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpefLA 149 query 158 YK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaivaag 216 :: :::::::::: :::: d1vl2a1 150 KFkTDLINYAMEK----------GIPI--------------------------------- 166 query 217 ydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1vl2a1 167 -------------------------------------------------- 167 FAST alignment (Normalized score: 7.91 Raw score:1662.00) query 1 DADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 59 :::::::::::::::::::::: ::: ::::::::: d1vl2a1 1 -----------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVANV 35 query 60 KYSSDHSKGDAAELARRTG-LNFRTVSIEPMFD-AYMA---SLGLTGL-------AEENL 107 :::: ::::::::::::: ::::::::::::: :::: :::: ::::: d1vl2a1 36 -GQKD-DFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRYLLGTAI 90 query 108 QSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG---------AY 151 ::::::::::::::::: :::::::::: :::: :: d1vl2a1 91 ARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALNPNLKVI 139 query 152 GPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILEL 201 :: :::::::::: d1vl2a1 140 SP-----WKDPEFLAKFKTDLINYAME--------------------------------- 161 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1vl2a1 162 ------------------------------------------------------------ 162 query 262 WREGH----- 266 d1vl2a1 162 -----KGIPI 166 TMalign alignment (TM-score: 0.47 Raw score:124.53) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 YSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D--VY 158 :::::::::::::: :::::::: : :::::::: :: :::::: : :: d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEFLA 149 query 159 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 218 :::::::::::: : : ::: d1vl2a1 150 -KFKTDLINYAME-K------G-IPI---------------------------------- 166 query 219 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vl2a1 167 ------------------------------------------------ 167 HHsearch alignment (Probability: 0.97 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 82 ::::::::::::::::::::::: ::: ::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK-GFD-VIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 83 TVSIEPMFDAYMASLGLTGLA--------EENLQSRLRGTTLMAISNQEGHIVLAPG--- 131 ::::::::::::::::::::: :::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 132 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRNRAA 173 :::::::::::::::::: ::: :::::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPNLKV-ISPWKDPEFLAKFKTDLINYAMEKGIPI 166
Intermediate <-- 2.197 --> Hit
DALI alignment (Z-score: 8.2 Raw score:538.70) d1vl2a1 1 KEKVVLAYSgGLDTSVILKWLCEKGFDVIAYVANvgqkdDFVAIkeKALKTgASKVYV-E 59 ::::::::: :::::::::::::::::::::::: ::::: ::::: :::::: : d1dv1a2 1 LDKIVIANR-GEIALRILRACKELGIKTVAVHSS-----ADRDL--KHVLL-ADETVCiG 51 d1vl2a1 60 DLRrefvtdyiftallgnamyegryllgtaiarpLIAKRQVEIAEKEGAQYVAHGATgkg 119 ::: ::::::::::::::::::::::: d1dv1a2 52 PAP--------------------------svksyLNIPAIISAAEITGAVAIHPGYG-fl 84 d1vl2a1 120 nDQVRFELTYAAlnPNLKVISpwkdpeflakfktdlinyamekgipi 166 ::::::::::: ::::::: d1dv1a2 85 sENANFAEQVER--SGFIFIG----------------pkaetirlmg 113 FAST alignment (Normalized score: 7.26 Raw score:994.20) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALK---------T 51 :::::::: :::::::::::::::::::::::: : d1dv1a2 1 LDKIVIAN-RGEIALRILRACKELGIKTVAVHS-----------------SADRDLKHVL 42 d1vl2a1 52 GASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAI----ARPL---IAKRQVEIAE 104 ::::::: :::: :::::::::: d1dv1a2 43 LADETVC--------------------------------IGPAPSVKSYLNIPAIISAAE 70 d1vl2a1 105 KEGAQYVAHGATGKGND-------QVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLIN 157 ::::::::: :::::::::: ::::: d1dv1a2 71 ITGAVAIHP--------GYGFLSENANFAEQVER--SGFIF------------------- 101 d1vl2a1 158 YAMEKGIPI------------ 166 d1dv1a2 102 ---------IGPKAETIRLMG 113 TMalign alignment (TM-score: 0.50 Raw score:82.68) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVED 60 ::::::::: :::::::::::::::::::::::: : :::: :::: ::::::::: d1dv1a2 1 LDKIVIANR-GEIALRILRACKELGIKTVAVHSS----A-DRDL--KHVL-LADETVCIG 51 d1vl2a1 61 LRREFVTDYIFTALLGNAMYEGRYLLGTAIA---RPLIAKRQVEIAEKEGAQYVAHGATG 117 :: : : : : : ::::::::::::::::::::: d1dv1a2 52 PA--P----------------------S--VKSYL-N-IPAIISAAEITGAVAIHPGYG- 82 d1vl2a1 118 KGNDQVRFELTYAALNP-NLKVISPWK---------DPEFLAKFKTDLINYAMEKGIPI 166 ::::: ::::::::: :::::: : d1dv1a2 83 --FLSEN-ANFAEQVERSGFIFIG--PKAETIRLMG----------------------- 113 HHsearch alignment (Probability: 0.13 E-value:0.03) d1vl2a1 91 ARPLIAKRQVEIAEKEGAQYVAHGATGKGNDQVRFELTYAALNPNLKVISP 141 ::::::::::::::::::::::::: ::::::::::::: :::::::::: d1dv1a2 57 KSYLNIPAIISAAEITGAVAIHPGY-GFLSENANFAEQV--ERSGFIFIGP 104