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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.669 --> Intermediate <-- 0.843 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1mvla_) 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 d1mvla_ 4'​-​phosphopantothenoylcysteine decarboxylase (PPC decarboxylase,​ halotolerance protein Hal3a)Homo-​oligomeric flavin-​containing Cys decarboxylases,​ HFCDHomo-​oligomeric flavin-​containing Cys decarboxylases,​ HFCDα/β

Supporting Alignments

Query <-- 1.669 --> Intermediate
DALI alignment (Z-score: 12.4 Raw score:948.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK---- 457 :::::::::::::::: :::::::: :::: :::: :::::: d1vl2a1 93 PLIAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpef 147 query 458 DVYK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaiva 516 :::: :::::::::: :::: d1vl2a1 148 LAKFkTDLINYAMEK----------GIPI------------------------------- 166 query 517 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1vl2a1 167 ---------------------------------------------------- 167 FAST alignment (Normalized score: 5.35 Raw score:1644.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 :::::::::::::::::::::: ::: ::::::: d1vl2a1 1 -------------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVA 33 query 360 PS-KYS-SDHSKGDAAELARRTG---LNFRTVSIEPMFD-AYMA---SLGLTGL------ 404 :: ::: :::::::::: ::::::::::::: :::: :::: d1vl2a1 34 NVGQKDDFVAIKEKALK------TGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRY 84 query 405 -AEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG----- 451 :::::::::::::::::::::: :::::::::: :::: d1vl2a1 85 LLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALN 133 query 452 ----AYGPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 497 :::: :::::::::: d1vl2a1 134 PNLKVISP-----WKDPEFLAKFKTDLINYAME--------------------------- 161 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 557 d1vl2a1 162 ------------------------------------------------------------ 162 query 558 LPITNRWREGH----- 568 d1vl2a1 162 -----------KGIPI 166 TMalign alignment (TM-score: 0.23 Raw score:131.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D-- 458 :::::::::::::::: :::::::: : :::::::: :: :::::: : d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEF 147 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 :: :::::::::::: : : ::: d1vl2a1 148 LA-KFKTDLINYAME-K------G-IPI-------------------------------- 166 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1vl2a1 167 -------------------------------------------------- 167 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 385 TVSIEPMFDAYM--------ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPG--- 433 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 434 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRN 472 ::::::::::::::: :::::: ::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPN-LKVISPWKDPEFLAKFKTDLINYAMEKG 163
Intermediate <-- 0.843 --> Hit
DALI alignment (Z-score: 3.7 Raw score:370.50) d1vl2a1 1 KEKVVLAY---sgGLDTSVILKWLCEkGFDVIAYVANVgqkddfvaIKEKALKtgaSKVY 57 :::::::: ::::::::::::: ::::::::::: ::::::: :::: d1mvla_ 1 KPRVLLAAsgsvaAIKFGNLCHCFTE-WAEVRAVVTKS---slhflDKLSLPQ--eVTLY 54 d1vl2a1 58 VEDLrrefvtdyiftallgnamyegryllgtaiarpliakrqvEIAEkeGAQYVAHGAtg 117 :::: :::: ::::::::: d1mvla_ 55 TDED------------------------ewsswnkigdpvlhiELRR--WADVLVIAP-l 87 d1vl2a1 118 kGNDQVRF---------eltYAALNPNLKVISPW-------------------------K 143 ::::::: :::::::::::::: : d1mvla_ 88 sANTLGKIagglcdnlltciIRAWDYTKPLFVAPamntlmwnnpfterhllsldelgitL 147 d1vl2a1 144 DPEflAKFK-----tdlinyamekgipi 166 ::: :::: d1mvla_ 148 IPP--IKNGamaepsliystvrlfwesq 173 FAST alignment (Normalized score: 2.52 Raw score:427.60) d1vl2a1 1 --KEKVVLAYSG------GLDTSVILKWLCEKGFDVIAYVANVGQKDDFVA-------IK 45 ::::: ::::::::::::: ::::::::: :: d1mvla_ 1 KPRVLLA-----ASGSVAAIKFGNLCHCFTE-WAEVRAVVT----------KSSLHFLDK 44 d1vl2a1 46 EKALKTGA----SKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR--------- 92 :: ::::: d1mvla_ 45 LS------LPQEVTLYT----------------------------------DEDEWSSWN 64 d1vl2a1 93 ------------------------PLIAK---------RQVEIAEKEGA-----QYVAHG 114 ::::: ::::::::: :::::: d1mvla_ 65 KIGDPVLHIELRRWADVLVIAPLSANTLGKIAGGLCDNLLTCIIRAW--DYTKPLFVAPA 122 d1vl2a1 115 AT---GKGNDQVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI----- 166 :: ::::::::::::::: :::::: d1mvla_ 123 MNTLMWNNPFTERHLLSLDE--LGITLI---------------------------PPIKN 153 d1vl2a1 167 -------------------- 167 d1mvla_ 154 GAMAEPSLIYSTVRLFWESQ 173 TMalign alignment (TM-score: 0.44 Raw score:72.34) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVANVGQ-KDDFVAIKEKALKTG-ASKV 56 :::::::::::::::::::::::: :::::::::: : :: :: :::::: :::: d1mvla_ 1 KPRVLLAASGSVAAIKFGNLCHCFTEWAEVRAVVTK--SS-LH--FL--DKLSLPQEVTL 53 d1vl2a1 57 YVEDLRR---------EFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEG 107 ::::::: :::::::: : d1mvla_ 54 YTDEDEWSSWNKIGDP---------------------------------VLHIELRR--W 78 d1vl2a1 108 AQYVAH-GATGKGNDQVRFELT---------YAALNPNLKVISPW--------------- 142 :::::: ::: :::::::::: :::::::::::::: d1mvla_ 79 ADVLVIAPLS--ANTLGKIAGGLCDNLLTCIIRAWDYTKPLFVAPAMNTLMWNNPFTERH 136 d1vl2a1 143 ----------KDPEFLAKFK-TDL-INY--------------AMEKGIPI 166 ::: :: :: :: :: d1mvla_ 137 LLSLDELGITLIP--PI-KNG-AMA-EPSLIYSTVRLFWESQ-------- 173 HHsearch alignment (Probability: 0.83 E-value:0.00) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCE--KGFDVIAYVANVGQK 38 ::::::::::::::::::::::: ::::::::::::::: d1mvla_ 1 KPRVLLAASGSVAAIKFGNLCHCFTEWAEVRAVVTKSSLH 40