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 <-- 1.875 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1f9aa_) 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 d1f9aa_ Nicotinamide mononucleotide (NMN) 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 <-- 1.875 --> Hit
DALI alignment (Z-score: 6.5 Raw score:659.40) d1mopa_ 1 ipafhpgelnvysapgdvadvsralrltgrRVMLVPTMG-ALHEGHLALVRAAKRVpgSV 59 ::::::::: :::::::::::::::: :: d1f9aa_ 1 ------------------------------LRGFIIGRFqPFHKGHLEVIKKIAEE-vDE 29 d1mopa_ 60 VVVSIFVNPmqfgaggDLDAYPR----TPDDDLAQLRAE-GVEIAFTPTTaamypdglrT 114 ::::::::: ::::::: :::::::::::: :::::::::: : d1f9aa_ 30 IIIGIGSAQ-----ksHTLENPFtageRILMITQSLKDYdLTYYPIPIKD--------iE 76 d1mopa_ 115 TVQpgplaaeleggprpthfagvlTVVLKLLQIV-RPDRVFFgekdyqQLVLIRQLVADf 173 ::: :::::::::: ::::::: ::::::::::: d1f9aa_ 77 FNS---------------------IWVSYVESLTpPFDIVYS------GNPLVRVLFEE- 108 d1mopa_ 174 nLDVAVVGVPTVREadgLAMSSR-NRYL-DPAQRaaavalsaaltaaahaatagaqaald 231 ::::::::::::: :::::: :::: ::::: d1f9aa_ 109 -RGYEVKRPEMFNR---KEYSGTeIRRRmLNGEK-------------------------- 138 d1mopa_ 232 aaravldaapgvavdylelrdiglgpmplngsgrllvaarlgttrlldniaieigtf 288 d1f9aa_ 139 -------------------------------wehlvpkavvdvikeikgverlrkla 164 FAST alignment (Normalized score: 5.15 Raw score:1119.00) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMG-ALHEGHLALVRAAKRVPG-- 57 ::::::::: :::::::::::::: d1f9aa_ 1 ------------------------------LRGFIIGRFQPFHKGHLEVIKKIA----EE 26 d1mopa_ 58 -SVVVVSIFVNPMQFGAGGDL-------DAYPR-TPDDDLAQLRAEGV--------EIAF 100 ::::::: ::::: ::::::::::: :::: d1f9aa_ 27 VDEIIIGI-------------GSAQKSHTLENPFTAGERILMITQ---SLKDYDLTYYPI 70 d1mopa_ 101 TPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFA---GVLTVVLKLLQI-VRPDRVFFG 156 ::: :::::::::::: ::::::: d1f9aa_ 71 PIK--------------------------------DIEFNSIWVSYVESLTPPFDIVY-- 96 d1mopa_ 157 EKDYQQ--LVLIRQLVADFNLDVAVVGVPTVREADGL----AMSSRNRYLDPAQRAAAVA 210 :::::::::: :::::::::: :::::::: d1f9aa_ 97 ------SGNPLVRVLFEE--RGYEVKRPEM-------FNRKEYSGTEIR----------- 130 d1mopa_ 211 LSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAA 270 d1f9aa_ 131 ------------------------------------------------------------ 131 d1mopa_ 271 RLGTTRLLDNIAIEIGTF---------------------------------- 288 d1f9aa_ 131 ------------------RRMLNGEKWEHLVPKAVVDVIKEIKGVERLRKLA 164 TMalign alignment (TM-score: 0.37 Raw score:106.51) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMG-ALHEGHLALVRAAKRVPGSV 59 ::::::::: ::::::::::::::::: :: d1f9aa_ 1 ------------------------------LRGFIIGRFQPFHKGHLEVIKKIAEEV-DE 29 d1mopa_ 60 VVVSIFVNPMQFGAGGDLDA--YPR---TP-DDDLAQLRAEGVEIAFTPTTAAMYPDGLR 113 ::::::::: : ::: ::: :: :::::::::::::::::::: :: : d1f9aa_ 30 IIIGIGSAQ--K-----SHTLENPFTAGERILMITQSLKDYDLTYYPIPIK--DI---E- 76 d1mopa_ 114 TTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIV-RPDRVFFGEKDYQQLVLIRQLVAD 172 ::: :: :::::::: ::::::: : ::::::::: d1f9aa_ 77 -FNS--------------------IW-VSYVESLTPPFDIVYS-G-----NPLVRVLFE- 107 d1mopa_ 173 FNLDVAVVGVPTVREADGLAMSSRN-RYL--DPA-QR----------------------- 205 : ::::::::::::: ::::::: ::: ::: : d1f9aa_ 108 E-RGYEVKRPEMFNR---KEYSGTEIRRRMLNGEK-WEHLVPKAVVDVIKEIKGVERLRK 162 d1mopa_ 206 -AAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSG 264 d1f9aa_ 163 L----------------------------------------------------------- 163 d1mopa_ 265 RLLVAARLGTTRLLDNIAIEIGTF 288 : d1f9aa_ 164 ----------A------------- 164 HHsearch alignment (Probability: 0.96 E-value:0.00) d1mopa_ 34 LVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRA 93 ::::::::::::::::::::: ::::::::::::::::::::::: :::::::::::::: d1f9aa_ 5 IIGRFQPFHKGHLEVIKKIAE-EVDEIIIGIGSAQKSHTLENPFT-AGERILMITQSLKD 62 d1mopa_ 94 EGVEIAFTPTTAAMYPDG 111 :::::::::::::::::: d1f9aa_ 63 YDLTYYPIPIKDIEFNSI 80