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 <-- 0.714 --> Intermediate <-- 0.864 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1nupa_) through the intermediate protein (d1mopa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1mopa_ Pantothenate synthetase (Pantoate-​beta-​alanine ligase,​ PanC)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1nupa_ Cytosolic NMN/​NAMN adenylyltransferaseNucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 0.714 --> Intermediate
DALI alignment (Z-score: 5.8 Raw score:745.80) query 1 -------dadeevysalvvglrayvaKNGFRSVLIGL-SGGI-DSALVAAIACDALgaqN 51 ::::::::::: :::: ::::::::::::: : d1mopa_ 1 ipafhpgelnvysapgdvadvsralrLTGRRVMLVPTmGALHeGHLALVRAAKRVP-gsV 59 query 52 VYGVSMPSK---------ysSDHSKGDAAELARRTGL-NFRTVSIEPMFDAYMA------ 95 ::::::::: ::::::::::::::::: :::::::::::::::: d1mopa_ 60 VVVSIFVNPmqfgaggdldaYPRTPDDDLAQLRAEGVeIAFTPTTAAMYPDGLRttvqpg 119 query 96 ----slgltgLAEENLQSRLRGTTLMAISNqeGHIVLAPGNkselavGYST--------l 143 :::::::::::::::::::: ::::::::: :::: d1mopa_ 120 plaaeleggpRPTHFAGVLTVVLKLLQIVR--PDRVFFGEK-----dYQQLvlirqlvad 172 query 144 ygdsvgAYGPiKDVY---kTSIFrlaewrnraaaergqtppipeaSITK-------pdYP 193 :::: :::: :::: :::: :: d1mopa_ 173 fnldvaVVGV-PTVReadgLAMS----------------------SRNRyldpaqraaAV 209 query 194 VLDAILELYvDRDT------GADAIVaAGYD---relvvKTLRmvDTAEYkrrqyppgtk 244 ::::::::: :::: :::::: :::: :::: ::::: d1mopa_ 210 ALSAALTAA-AHAAtagaqaALDAAR-AVLDaapgvavdYLEL--RDIGL---------- 255 query 245 isakgfgkdrrlpITNRWR-----------------------egh 266 :::::: d1mopa_ 256 ------------gPMPLNGsgrllvaarlgttrlldniaieigtf 288 FAST alignment (Normalized score: 3.14 Raw score:869.40) query 1 DADEEVYSALVVGLRAYVAKNGF------------------------------RSVLIGL 30 ::::::: d1mopa_ 1 -----------------------IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPT 37 query 31 S--GGIDSALVAAIACDALGAQ--NVYGVSMPS-----------KYSSDHSKGDAAELAR 75 : :::::::::::::::: :::::::: ::::: :::::::::: d1mopa_ 38 MGALHEGHLALVRAAKRVP---GSVVVVSIFV-NPMQFGAGGDLDAYPR-TPDDDLAQLR 92 query 76 RTGL-NFRTVSIEPM-FDAYMASLGL------------------TGLAEENLQSRLRGTT 115 :::: ::::: :::: :::::: :::::::::::::::: d1mopa_ 93 AEGVEIAFTP-TTAAMYPDGLR----TTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQI 147 query 116 LMAISNQEG---HIVLAPGNKSELAVGYSTLYGDSVG----------------------A 150 :::::: : d1mopa_ 148 ---------VRPDRVFFG-------------------EKDYQQLVLIRQLVADFNLDVAV 179 query 151 YGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP-------------------- 190 ::: d1mopa_ 180 VGV-------------------------------------PTVREADGLAMSSRNRYLDP 202 query 191 --------DYPVLDAILELYVDRDTGADAIVAAG-----YDRELVVKTLRMVDTAEYKRR 237 ::::::::: :::::::::::::: d1mopa_ 203 AQRAAAVALSAALTAAA-----------------HAATAGAQAALDAARAVLD------- 238 query 238 QYPPGTKISAKGFGKDRRLPITNRWREGH------------------------------- 266 d1mopa_ 239 -----------------------------AAPGVAVDYLELRDIGLGPMPLNGSGRLLVA 269 query 267 ------------------- 267 d1mopa_ 270 ARLGTTRLLDNIAIEIGTF 288 TMalign alignment (TM-score: 0.50 Raw score:134.27) query 1 ----------------------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSG 32 ::::::::::: d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLT---------------------GRRVMLVPTMG 39 query 33 -GI-DSALVAAIACDALGAQNVYGVSMPSK--------YS-SDHSKGDAAELARRTGL-N 80 :: :::::::::: ::::::::::::::: :: ::::::::::::::::: : d1mopa_ 40 ALHEGHLALVRAAK-RVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEI 98 query 81 FRTVSIEPMFDAYMASL-GL-----------TGLAEENLQSRLRGTTLMAISNQEGHIVL 128 ::::::::::::::::: : ::::::::::::::::::::: ::::: d1mopa_ 99 AFTPTTAAMYPDGLRTTV-QPGPLAAELEGG-PRPTHFAGVLTVVLKLLQIVR--PDRVF 154 query 129 APGNKSELAVGYSTLYGDSVG-----------AYGPIKDVYKTSIFRLAEWRNRAAAERG 177 :::: :: : : ::::: ::::: :::::::::: d1mopa_ 155 FGEK--DY--Q--Q--LVLIRQLVADFNLDVAVVGVP--TVREADGLAM----------- 193 query 178 QTPPIPEASITK-----P--DYPVLDAILELYVDRD-----TGADAIVAAGYDRE--LVV 223 ::::: : :::::::::::::::: :::::::: ::::: ::: d1mopa_ 194 -------SSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARA-VLDAAPGVAV 245 query 224 KTLRMVDTAEYKRR----------------------QYPPGTKISAKGFGKDRR--LPIT 259 ::: :::::::::: :::: :: d1mopa_ 246 DYL-ELRDIGLGPMPLNGSGRLLVAARLGTTRLLDN----------IAIE--IGTF---- 288 query 260 NRWREGH 266 d1mopa_ 289 ------- 289 HHsearch alignment (Probability: 0.01 E-value:0.62) query 53 YGVSMPSKYSSDHSKGDAAELARRT 77 ::::::::::::::::::::::::: d1mopa_ 191 LAMSSRNRYLDPAQRAAAVALSAAL 215
Intermediate <-- 0.864 --> Hit
DALI alignment (Z-score: 6.5 Raw score:697.30) d1mopa_ 1 ipafhpgelnvysapgdvadvsralrlTGRRVMLVPTMG-ALHEGHLALVRAAKRV---- 55 :::::::::::: :::::::::::::::: d1nupa_ 1 --------------------------sRIPVVLLACGSFnPITNMHLRMFEVARDHlhqt 34 d1mopa_ 56 --PGSV-VVVSIFvNPMQFgaggdLDAYP---RTPDDDLAQLRAEGVEIAFTP--TTAAM 107 :::: :::::: ::::: ::::: ::::::::::::::::::::: ::::: d1nupa_ 35 gmYQVIqGIISPV-NDTYG-----KKDLAashHRVAMARLALQTSDWIRVDPWesEQAQW 88 d1mopa_ 108 ypdglrttvqpgplaaeleggprpthfagvlTVVLKLLQIVR-------pDRVFFGEKDY 160 ::::::::::: :::::::::: d1nupa_ 89 -------------------------------METVKVLRHHHskllavpeLKLLCGADVL 117 d1mopa_ 161 QQLV----lirQLVAdfnLDVAVVGVPT------------------------vreadGLA 192 :::: :::: :::::::::: ::: d1nupa_ 118 KTFQtpnlwkdAHIQeivEKFGLVCVGRvshdpkgyiaespilrmhqhnihlakepvQNE 177 d1mopa_ 193 MSSR-NRYL-DPAQRaaavalsaaltaaahaatagaqaaldaaravldaapgvavdylel 250 :::: :::: ::::: d1nupa_ 178 ISATyIRRAlGQGQS--------------------------------------------- 192 d1mopa_ 251 rdiglgpmplngsgrllvaarlgttrlldniaieigtf 288 d1nupa_ 193 -----------------vkylipdavityikdhglytk 213 FAST alignment (Normalized score: 2.84 Raw score:703.40) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRL-TGRRVMLVPTMG-ALHEGHLALVRAAKRVPG- 57 :::::::::::: :::::::::::::: d1nupa_ 1 ---------------------------SRIPVVLLACGSFNPITNMHLRMFEVAR----D 29 d1mopa_ 58 ----------SVVVVSIFVNPMQFGAGGDL-----DAYPR-TPDDDLAQLRAEGV----- 96 ::::::: ::::: ::::::::::: d1nupa_ 30 HLHQTGMYQVIQGIISP-------------VNDTYGKKDLAASHHRVAMARL---ALQTS 73 d1mopa_ 97 --EIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGP------------------------- 129 :::: d1nupa_ 74 DWIRVD-----------------------------PWESEQAQWMETVKVLRHHHSKLLA 104 d1mopa_ 130 -----------------RPTHFAG-VLTVVLKLLQIVRPDRVFFGEKDYQQLV-----LI 166 :::: :::::::::::: ::::: :: d1nupa_ 105 VPELKLLCGADVLKTFQTPNL---WKDAHIQEIVEKF---GLVCV--------GRVSHDP 150 d1mopa_ 167 RQLVADFNL--------DVAVVGVPTVREADGL----AMSSRNRYLDPAQRAAAVALSAA 214 ::::::: ::::::: :::::: d1nupa_ 151 KGYIAES--PILRMHQHNIHLAKE---------PVQNEISATY----------------- 182 d1mopa_ 215 LTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGT 274 d1nupa_ 183 ------------------------------------------------------------ 183 d1mopa_ 275 TRLLDNIAIEIGTF------------------------------- 288 d1nupa_ 183 --------------IRRALGQGQSVKYLIPDAVITYIKDHGLYTK 213 TMalign alignment (TM-score: 0.37 Raw score:106.39) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMG-ALHEGHLALVRAAKR-VP-- 56 ::::::::::::: ::::::::::::::: :: d1nupa_ 1 --------------------------SRIPVVLLACGSFNPITNMHLRMFEVARDHLHQT 34 d1mopa_ 57 ---GSVVVVSIFVNPMQFGAGGDLDAYP-R--TPDDDLAQLRAEGVEIAFT-P--TTAAM 107 :::::::::::::::: : ::: : ::::::::::::::::::: : ::::: d1nupa_ 35 GMYQVIQGIISPVNDTYGK---K--DLAASHHRVAMARLALQTSDWIRVDPWESEQAQWM 89 d1mopa_ 108 Y----------------------------PDGLRTTVQPGPLAAELEGGPRPTHFAGVLT 139 : ::: : :: :: :: d1nupa_ 90 ETVKVLRHHHSKLLAVPELKLLCGADVLK--------TFQ--T--------PN--LW-KD 128 d1mopa_ 140 -VVLKLLQIVRPDRVFFGEKDYQQLVLIR--QLVADFNLDVAVVGVP-TVREADGLAMSS 195 :::::::::: :::::::::: ::::: :::::::::::::::: ::: :::: d1nupa_ 129 A-HIQEIVEKFG-LVCVGRVSHD-PKGYIAESPILRMHQHNIHLAKEPVQN-----EISA 180 d1mopa_ 196 RN-RYL--DPA-QR-------------------AAAVALSAALTAAAHAATAGAQAALDA 232 :: ::: ::: : d1nupa_ 181 TYIRRALGQGQS-VKYLIPDAVITYIKDHGLYT--------------------------- 212 d1mopa_ 233 ARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTF 288 : d1nupa_ 213 ------------------------------------------K------------- 213 HHsearch alignment (Probability: 0.67 E-value:0.00) d1mopa_ 30 RRVMLVP-TMGALHEGHLALVRAAKRVPGS---VVVVSIFVNPMQFGAG 74 ::::::: :::::::::::::::::::::: :::::::::::::::: d1nupa_ 4 PVVLLACGSFNPITNMHLRMFEVARDHLHQTGMYQVIQGIISPVNDTYG 52