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 <-- 0.611 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1qwja_) 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 d1qwja_ CMP acylneuraminate synthetaseNucleotide-​diphospho-​sugar transferasesNucleotide-​diphospho-​sugar transferasesα/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 <-- 0.611 --> Hit
DALI alignment (Z-score: 3.1 Raw score:391.90) d1mopa_ 1 ipafhpgelnvysapgdvadvsralrlTGRRVMLVPTMG--------ALHE-----GHLA 47 :::::::::::: :::: :::: d1qwja_ 1 ---------------------------PPHLAALVLARGgskgiplkNIKRlagvpLIGW 33 d1mopa_ 48 LVRAAKRVPGS-VVVVSIFvnpmqfgaggdldayprtPDDDLAQLRAEGVEIAFTPTTaa 106 ::::::::::: ::::::: ::::::::::::::::::::: d1qwja_ 34 VLRAALDAGVFqSVWVSTD------------------HDEIENVAKQFGAQVHRRSSE-- 73 d1mopa_ 107 mypdglrttvqpgplaaeleggprpthfagvlTVVLKLLQIVR-------pDRVFFGEK- 158 ::::::::::: :::::::: d1qwja_ 74 ---------------------------tskdsSTSLDAIVEFLnyhnevdiVGNIQATSp 106 d1mopa_ 159 ------------------------------------------------------------ 159 d1qwja_ 107 clhptdlqkvaemireegydsvfsvvrrhqfrwseiqkgvrevteplnlnpakrprrqdw 166 d1mopa_ 159 ----dYQQL-------vlirqLVAD---fnldvavvgvPTVR--EADGLAmssrnryldp 202 :::: :::: :::: :::::: d1qwja_ 167 dgelyENGSfyfakrhliemgYLQGgkmayyemraehsVDIDvdIDWPIA---------- 216 d1mopa_ 203 aqraaavalsaaltaaahaatagaqaaldaaravldaapgvavdylelrdiglgpmplng 262 d1qwja_ 217 ------------------------------------------------------------ 217 d1mopa_ 263 sgrllvaarlgttrlldniaieigtf 288 d1qwja_ 217 --------------eqrvlrfgyfgk 228 FAST alignment (Normalized score: 2.63 Raw score:673.40) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLT-GRRVMLVPTMGALH----------------- 42 ::::::::: d1qwja_ 1 ----------------------------PPHLAALVLA-----RGGSKGIPLKNIKRLAG 27 d1mopa_ 43 -EGHLALVRAAKRVPG-SVVVVSIFVNPMQFGAGGDLDAYPRT-PDDDLAQLRAEGVEIA 99 ::::::::::::::: ::::::: ::::::::::::: :: d1qwja_ 28 VPLIGWVLRAALDAGVFQSVWVST-------------------DHDEIENVAKQFGA-QV 67 d1mopa_ 100 FTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFA-------GVLTVVLKLLQIVRP-- 150 ::::: ::::::::::::: d1qwja_ 68 HRRSS-------------------------------ETSKDSSTSLDAIVEFLNYH--NE 94 d1mopa_ 151 ---DRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAA 207 ::::: d1qwja_ 95 VDIVGNIQ---------------------------------------------------- 102 d1mopa_ 208 AVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLL 267 d1qwja_ 103 ------------------------------------------------------------ 103 d1mopa_ 268 VAARLGTTRLLDNIAIEIGTF--------------------------------------- 288 d1qwja_ 103 ---------------------ATSPCLHPTDLQKVAEMIREEGYDSVFSVVRRHQFRWSE 141 d1mopa_ 289 ------------------------------------------------------------ 289 d1qwja_ 142 IQKGVREVTEPLNLNPAKRPRRQDWDGELYENGSFYFAKRHLIEMGYLQGGKMAYYEMRA 201 d1mopa_ 289 --------------------------- 289 d1qwja_ 202 EHSVDIDVDIDWPIAEQRVLRFGYFGK 228 TMalign alignment (TM-score: 0.30 Raw score:85.20) d1mopa_ 1 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVV 60 :::: d1qwja_ 1 -----------------------------PPHL--------------------------- 4 d1mopa_ 61 VVSIFVNPMQFGAGGDLDAY-P-----RTPDDDLAQLRAEGVE-IAFTPTTA-------- 105 ::::::::: :: :: :::: : :::::::::::::::: :::::::: d1qwja_ 5 AALVLARGG-SK-GI-PLKNIKRLAGVPLIGWVLRAALDAGVFQSVWVSTDHDEIENVAK 61 d1mopa_ 106 -------AMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVR-PDRV---- 153 ::: :: :: ::: ::::::::::::::: :::: d1qwja_ 62 QFGAQVHRRS--SE--TS--------------KDS-STSLDAIVEFLNYHNEVDIVGNIQ 102 d1mopa_ 154 -------------------------FFGE------------------------------- 157 :::: d1qwja_ 103 ATSPCLHPTDLQKVAEMIREEGYDSVFSVVRRHQFRWSEIQKGVREVTEPLNLNPAKRPR 162 d1mopa_ 158 ---------KDY-QQL--VLIR-QLVADFNL-DVAVVGVPTVREADGLAMSSR-NRYL-- 200 ::: :: :: ::::::: ::::::::::: :::::: :::: d1qwja_ 163 RQDWDGELYENGS-FYFA--KRH-LIEMGYLQ-GGKMAYYEMRA---EHSVDIDVDIDWP 214 d1mopa_ 201 DP--AQR---------AAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLE 249 :: : d1qwja_ 215 IAEQ--RVLRFGYFGK-------------------------------------------- 228 d1mopa_ 250 LRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTF 288 d1qwja_ 229 --------------------------------------- 229 HHsearch alignment (Probability: 0.00 E-value:1.40) d1mopa_ 143 KLLQIVRPDRVFFGEKDYQQL 163 ::::::::::::::::::::: d1qwja_ 96 DIVGNIQATSPCLHPTDLQKV 116