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 <-- 1.261 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1kama_) 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 d1kama_ 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 <-- 1.261 --> Hit
DALI alignment (Z-score: 5.8 Raw score:586.90) d1mopa_ 1 ipafhpgelnvysapgdvadvsralrltGRRVMLVPTMG-ALHEGHLALVRAAKRVPGS- 58 ::::::::::: ::::::::::::::::::: d1kama_ 1 ----------------------------SKKIGIFGGTFdPPHNGHLLMANEVLYQAGLd 32 d1mopa_ 59 VVVVSIFVNPmqfgaggdldaypRTPDDDLAQLRAEGVEIAFTP-TTAAMypdglrttvq 117 :::::::::: ::::::::::::::::::::: ::::: d1kama_ 33 EIWFMPNQIP----------dsfHRVEMLKLAIQSNPSFKLELVeMEREG---------- 72 d1mopa_ 118 pgplaaeleggprpthfagvlTVVLKLLQIVR------pDRVFFGEkdyqQLVL-irqlv 170 ::::::::::: ::::::: :::: d1kama_ 73 --------------------pSYTFDTVSLLKqrypndqLFFIIGA----DMIEylpkwy 108 d1mopa_ 171 ADFNL--DVAVVGVP-----------------TVREadglaMSSRN-RYLD-PAQRaaav 209 ::::: :::::::: :::: ::::: :::: :::: d1kama_ 109 KLDELlnLIQFIGVKrpgfhvetpypllfadvPEFE-----VSSTMiRERFkSKKP---- 159 d1mopa_ 210 alsaaltaaahaatagaqaaldaaravldaapgvavdylelrdiglgpmplngsgrllva 269 d1kama_ 160 ----------------------------------------------------------td 161 d1mopa_ 270 arlgttrlldniaieigtf 288 d1kama_ 162 ylipdkvkkyveenglyes 180 FAST alignment (Normalized score: 3.60 Raw score:820.30) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMG-ALHEGHLALVRAAKRVPG-- 57 ::::::::::: :::::::::::::: d1kama_ 1 ----------------------------SKKIGIFGGTFDPPHNGHLLMANEVL----YQ 28 d1mopa_ 58 ---SVVVVSIFVNPMQFGAGGDLDAYP---RTPDDDLAQLRAEGV-------EIAFTPTT 104 ::::::: :::::::::::: ::::: d1kama_ 29 AGLDEIWFMP-----------------NQIPDSFHRVEMLKL---AIQSNPSFKLEL--- 65 d1mopa_ 105 AAMYPDGLRTTVQPGPLAAELEGGPRPTHFA---------GVLTVVLKLLQIVRP----D 151 ::::::::::::: : d1kama_ 66 -------------------------------VEMEREGPSYTFDTVSLLKQRY--PNDQL 92 d1mopa_ 152 RVFFGEKDYQQ----------LVLIRQLVADFNLDVAVVGVPTVREADGL---------- 191 ::::::: :::::: :::::: d1kama_ 93 FFIIGAD----MIEYLPKWYKLDELLN-------LIQFIG----------VKRPGFHVET 131 d1mopa_ 192 ------------AMSSRNRY-----LDPAQRAAAVALSAALTAAAHAATAGAQAALDAAR 234 ::::: :::: d1kama_ 132 PYPLLFADVPEFEVSST---MIRERFKSK------------------------------- 157 d1mopa_ 235 AVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTF------ 288 d1kama_ 158 ------------------------------------------------------KPTDYL 163 d1mopa_ 289 ----------------- 289 d1kama_ 164 IPDKVKKYVEENGLYES 180 TMalign alignment (TM-score: 0.36 Raw score:102.80) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMG-ALHEGHLALVRAAKR-VPGS 58 ::::::::::: ::::::::::::::: :::: d1kama_ 1 ----------------------------SKKIGIFGGTFDPPHNGHLLMANEVLYQAGLD 32 d1mopa_ 59 VVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTP-TTAAMYPDGLRTTVQ 117 ::::::: ::: : ::::::::::::::::::::::: :::::: d1kama_ 33 EIWFMPN-QIP--------D-SFHRVEMLKLAIQSNPSFKLELVEMEREGP--------- 73 d1mopa_ 118 PGPLAAELEGGPRPTHFAGVLTVVLKLLQIVR------PDRVFFGEKDYQQLVL-IR--Q 168 ::::::::::: :::::::: : ::: : : d1kama_ 74 ---------------------SYTFDTVSLLKQRYPNDQLFFIIGA--D--MIEY-LPKW 107 d1mopa_ 169 -LVADF-NLDVAVVGVP----------------TVREADGLAMSSRN-RYL--DPA---- 203 ::::: :::::::::: ::: :::::: ::: ::: d1kama_ 108 YKLDELLNLIQFIGVKRPGFHVETPYPLLFADVPEF-----EVSSTMIRERFKSKKPTDY 162 d1mopa_ 204 ------------------QRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAV 245 d1kama_ 163 LIPDKVKKYVEENGLYES------------------------------------------ 180 d1mopa_ 246 DYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTF 288 d1kama_ 181 ------------------------------------------- 181 HHsearch alignment (Probability: 0.77 E-value:0.00) d1mopa_ 30 RRVMLVPT-MGALHEGHLALVRAAKRVPGS--VVVVSI 64 :::::::: ::::::::::::::::: ::: :::::: d1kama_ 2 KKIGIFGGTFDPPHNGHLLMANEVLY-QAGLDEIWFMP 38