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 <-- 1.100 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1j6ua1) 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 d1j6ua1 UDP-​N-​acetylmuramate-​alanine ligase MurCMurCD N-​terminal domainMurCD N-​terminal 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 <-- 1.100 --> Hit
DALI alignment (Z-score: 6.5 Raw score:404.20) d1vl2a1 1 KEKVVLA-YSGGlDTSVILKWLCEKGFDVIAYVANvgqkddFVAIKEKALKTGAsKVYVE 59 ::::::: :::: :::::::::::::::::::::: ::::::::::::: ::::: d1j6ua1 1 HMKIHFVgIGGI-GMSAVALHEFSNGNDVYGSNIE------ETERTAYLRKLGI-PIFVP 52 d1vl2a1 60 dlrrefvtdyiftallgnamyegryllgtaiarplIAKRqvEIAEkegAQYVAHGATgkg 119 :::: :::: ::::::::: d1j6ua1 53 -----------------------------------HSAD--NWYD---PDLVIKTPA--- 69 d1vl2a1 120 ndQVRF--ELTYAAlnPNLKVISpwkdpeflakfktdlinyamekgipi 166 :::: :::::: ::::::: d1j6ua1 70 -vRDDNpeIVRARM--ERVPIEN-------------------------- 89 FAST alignment (Normalized score: 5.51 Raw score:669.90) d1vl2a1 1 KEKVVLAY--SGGLDTSVILKWLCEKGFDVIAYVANVGQKDD--FVAIKEKALKTGASKV 56 :::::: :::::::::::::::::::::::: :::::::::::: ::: d1j6ua1 1 HMKIHF--VGIGGIGMSAVALHEFSNGNDVYGSN--------IEETERTAYLRKLG-IPI 49 d1vl2a1 57 YVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAE-------KEGAQ 109 : ::::: d1j6ua1 50 F-----------------------------------------------VPHSADNWYDPD 62 d1vl2a1 110 YVAHGATGKGNDQ-------VRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEK 162 :::: ::::::::: :::::: d1j6ua1 63 LVIK---------TPAVRDDNPEIVRARM--ERVPIE----------------------- 88 d1vl2a1 163 GIPI- 166 d1j6ua1 89 ----N 89 TMalign alignment (TM-score: 0.39 Raw score:65.15) d1vl2a1 1 KEKVVLA-YSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVE 59 ::::::: :::: :::::::::::::::::::::: :::::::::: :::::::: d1j6ua1 1 HMKIHFVGIGGI-GMSAVALHEFSNGNDVYGSNIE------ETERTAYLRK-LGIPIFVP 52 d1vl2a1 60 DLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVE-IAEKEGAQYVAHGATGK 118 : : : :: :::::::::: d1j6ua1 53 -----------------------------------H--S--ADNW--YDPDLVIKTP--- 68 d1vl2a1 119 GNDQVRF--ELT-YA-ALNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI 166 :: :: : :: :::::::::: d1j6ua1 69 --AV-RDDN--PEIVRARMERVPIEN-------------------------- 89 HHsearch alignment (Probability: 0.08 E-value:0.06) d1vl2a1 3 KVVLAYSGGLDTSVILKWLCEKGFDVIAYV 32 :::::::::::::::::::::::::::::: d1j6ua1 3 KIHFVGIGGIGMSAVALHEFSNGNDVYGSN 32