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 <-- 1.963 --> Intermediate <-- 0.840 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1vhqa_) through the intermediate protein (d1jgta1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jgta1 beta-​Lactam synthetaseAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1vhqa_ Putative sigma cross-​reacting protein 27A (SCRP-​27A,​ EllB)Class I glutamine amidotransferase-​likeFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 1.963 --> Intermediate
DALI alignment (Z-score: 10.5 Raw score:1021.00) query 1 -----------DADEEVYSALVVGLRAYVAknGFRSVLIGLSGGIDSALVAAIACDALGA 49 ::::::::::::::::::: :::::::::::::::::::::::::::: d1jgta1 1 pglsrrilpegEAVAAVRAALEKAVAQRVT--PGDTPLVVLSGGIDSSGVAACAHRAAGE 58 query 50 qnVYGVSMPSKYSSdhSKGDAAELARRTGLNFRTVSIE-PMFDAYMA---slglTGLAEE 105 :::::::::::: :::::::::::::::::::::: :::::::: :::::: d1jgta1 59 --LDTVSMGTDTSN--EFREARAVVDHLRTRHREITIPtTELLAQLPyavwaseSVDPDI 114 query 106 NLQSRLRGTTLMAIsNQEGHIVLAPG-NKSELA--------------------------- 137 :::::::::::::: ::::::::::: :::::: d1jgta1 115 IEYLLPLTALYRAL-DGPERRILTGYgADIPLGgmhredrlpaldtvlahdmatfdglne 173 query 138 vgystlygdsvGAYGPIKD-------------------vyKTSIFRLAEWRnraaaergq 178 :::::::: ::::::::::: d1jgta1 174 mspvlstlaghWTTHPYWDrevldllvsleaglkrrhgrdKWVLRAAMADA--------- 224 query 179 tppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrq 238 :::::::: d1jgta1 225 ---LPAETVNR-------------------pklssfsrllldhgvaedrvheakrqvvre 262 query 239 yppgtkisakgfgkdrrlpitnrwregh 266 d1jgta1 263 lfdltvgggrhpsevdtddvvrsvadrt 290 FAST alignment (Normalized score: 6.65 Raw score:1846.00) query 1 D--------ADEEVYSALVVGLRAYVAKNGF-----RSVLIGLSGGIDSALVAAIACDAL 47 ::::::::::::::::::: :::::::::::::::::::::::: d1jgta1 1 -PGLSRRILPEGEAVAAVRAALEKAVAQ---RVTPGDTPLVVLSGGIDSSGVAACAHRAA 56 query 48 GAQ-NVYGVSMPSKYSSDH---SKGDAAELARRTGLNFRTVS-IEPMFDAYMASLGL--- 99 :::::::::: :::::::::::::::::::: :::::::: d1jgta1 57 ---GELDTVSMGTD-----TSNEFREARAVVDHLRTRHREITIPTTELLAQ------LPY 102 query 100 ---------TGLAEENLQSRLRGTTLMAISN--QEGHIVLAPGNKSELAVGYSTLYGDSV 148 :::::::::::::::: ::::::::: d1jgta1 103 AVWASESVDPDIIEYLLPLTALYRA------LDGPERRILTG------------------ 138 query 149 G-----------------------------------------------AYGPIKDVY--- 158 ::::: d1jgta1 139 -YGADIPLGGMHREDRLPALDTVLAHDMATFDGLNEMSPVLSTLAGHWTTHPY----WDR 193 query 159 --------------------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAI 198 ::::::::: ::::::::: d1jgta1 194 EVLDLLVSLEAGLKRRHGRDKWVLRAAMA------------DALPAETVN---------- 231 query 199 LELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPI 258 d1jgta1 232 ------------------------------------------------------------ 232 query 259 TNRWREGH---------------------------------------------------- 266 d1jgta1 232 --------RPKLSSFSRLLLDHGVAEDRVHEAKRQVVRELFDLTVGGGRHPSEVDTDDVV 283 query 267 ------- 267 d1jgta1 284 RSVADRT 290 TMalign alignment (TM-score: 0.50 Raw score:132.17) query 1 ----------DA-DEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGA 49 :: ::::::::::::::::: ::::::::::::::::::::::::::: d1jgta1 1 PGLSRRILPEGEAVAAVRAALEKAVAQRVT--PGDTPLVVLSGGIDSSGVAACAHRAAG- 57 query 50 QNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLG---------LT 100 : :::::::::::: :::::::::::::::::::::: ::::::::: d1jgta1 58 E-LDTVSMGTDTSN--EFREARAVVDHLRTRHREITIP--TTELLAQLPYAVWASESV-- 110 query 101 GLAEENLQSRLRGTTLMAISNQEGHIVLAP-GN--KSEL-------------A--VG-YS 141 ::::::::::::::::::: ::::::::: :: :::: : :: :: d1jgta1 111 -DPDIIEYLLPLTALYRALD-GPERRILTGYGADIPLGGMHREDRLPALDTVLAHDMATF 168 query 142 ---TLYGDSVG---------AYGPIK----D--V-------Y------KTSIFRLAEWRN 170 ::::: :::::: : : : ::::::::: :: d1jgta1 169 DGL---NEMSPVLSTLAGHWTTHPYWDREVLDLLVSLEAGLKRRHGRDKWVLRAAMA-DA 224 query 171 RAAAERGQTPPIPEASITKPDY-------------------------------------- 192 ::::::::: :: d1jgta1 225 ----------LPAETVNRP-KLSSFSRLLLDHGVAEDRVHEAKRQVVRELFDLTVGGGRH 273 query 193 -----------------PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYK 235 d1jgta1 274 PSEVDTDDVVRSVADRT------------------------------------------- 290 query 236 RRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1jgta1 291 ------------------------------- 291 HHsearch alignment (Probability: 0.96 E-value:0.00) query 2 ADEEVYSALVVGLRAYVAK--NGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 59 ::::::::::::::::::: :::::::::::::::::::::::::: :::::::::: d1jgta1 9 PEGEAVAAVRAALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRA--AGELDTVSMG- 65 query 60 KYSSDHSKGDAAELARRTGLNFRTVSI--EPMFDAYMASLGLTGL-AEENLQSRLRGTTL 116 :::::::::::::::::::::::::: :::::::::::::::: :::::::::::::: d1jgta1 66 -TDTSNEFREARAVVDHLRTRHREITIPTTELLAQLPYAVWASESVDPDIIEYLLPLTAL 124 query 117 MAISNQEGHIVLAPGNKSELAVGY 140 :::::::::::::::::::::::: d1jgta1 125 YRALDGPERRILTGYGADIPLGGM 148
Intermediate <-- 0.840 --> Hit
DALI alignment (Z-score: 2.6 Raw score:348.90) d1jgta1 1 pglsrrilpegeavaavraalekavaqrvtpGDTPLVVLSG--------GIDSSGVAACA 52 :::::::::: ::::::::::: d1vhqa_ 1 -------------------------------MKKIGVILSGcgvydgseIHEAVLTLLAI 29 d1jgta1 53 HRAAGELDTVSMGT---------------dtsNEFREARAVVDhlrtrHREITipttell 97 :::::::::::::: ::::::::::: ::::: d1vhqa_ 30 SRSGAQAVCFAPDKqqvdvinhltgeamtetrNVLIEAARITR---geIRPLA------- 79 d1jgta1 98 aqlpyavwasesvdpdiieyllpltalyralDGPER-RILTG------------------ 138 ::::: ::::: d1vhqa_ 80 -----------------------------qaDAAELdALIVPggfgaaknlsnfaslgse 110 d1jgta1 139 ----------------------YGAD--------------IPLGgmhredrlpalDTVLA 162 :::: :::: ::::: d1vhqa_ 111 ctvdrelkalaqamhqagkplgFMXIapamlpkifdfplrLTIG----------tDIDTA 160 d1jgta1 163 HDMATFDglnemspvlstlaghwtthpywdrEVLDllvsleaglkrrhgrDKWVLRAAMA 222 ::::::: :::: :::::::::: d1vhqa_ 161 EVLEEMG---------------aehvpcpvdDIVV--dednkivttpaymLAQNIAEAAS 203 d1jgta1 223 dalpaetvnrpklssfsrllldhgvaedrvheakrqvvrelfdltvgggrhpsevdtddv 282 d1vhqa_ 204 ------------------------------------------------------gidklv 209 d1jgta1 283 vrsvadrt 290 d1vhqa_ 210 srvlvlae 217 FAST alignment (Normalized score: 2.10 Raw score:526.70) d1jgta1 1 PGLSRRILPEGEAVAAVRAALEKAVAQRVTPGDTPLVVLSG---------GIDSSGVAAC 51 ::::::::: :::::::::: d1vhqa_ 1 -------------------------------MKKIGVILS-GCGVYDGSEIHEAVLTLLA 28 d1jgta1 52 AHRAA--GELDTVSMGTDTS-------------------NEFREARAVVDHLRT---RHR 87 ::: ::::::::: ::::::::: ::: d1vhqa_ 29 ISR--SGAQAVCFAPD----KQQVDVINHLTGEAMTETRNVLIEAARI------TRGEIR 76 d1jgta1 88 EITIPTTELLAQLPYAVWASESVDPDI--------------------------------- 114 : d1vhqa_ 77 P--------------------------LAQADAAELDALIVPGGFGAAKNLSNFASLGSE 110 d1jgta1 115 IEYLLPLTALYRALD---GPERRILTGYGADIPLGGMHREDR------------------ 153 :::::::::::: ::::::: d1vhqa_ 111 CTVDRELKALAQ---AMHQAGKPLG-----------------FMAIAPAMLPKIFDFPLR 150 d1jgta1 154 -----LPALDTVLAHDMATFDGLNEMSPVLSTL------------------AGHWTTHPY 190 :::::::::: ::::::::: d1vhqa_ 151 LTIGTDIDTAEVLEE------------------MGAEHVPCPVDDIVVDEDNKIVTTPAY 192 d1jgta1 191 WDREVLDLLVSLEAGLKRRHGRDKWVLRAAMADALPAETVNRPKLSSFSRLLLDHGVAED 250 d1vhqa_ 193 ------------------------------------------------------------ 193 d1jgta1 251 RVHEAKRQVVRELFDLTVGGGRHPSEVDTDDVVRSVADRT-------------------- 290 d1vhqa_ 193 ----------------------------------------MLAQNIAEAASGIDKLVSRV 212 d1jgta1 291 ----- 291 d1vhqa_ 213 LVLAE 217 TMalign alignment (TM-score: 0.31 Raw score:90.04) d1jgta1 1 PGLSRRILPEGEAVAAVRAALEKAVAQRVTPGDTPLVVLS-G-----GI--DSSGVAACA 52 ::::::::: : :: ::::::::: d1vhqa_ 1 -------------------------------MKKIGVILSGCGVYDGSEIHEAVLTLLAI 29 d1jgta1 53 HRAAGELDTVSMGTDTS---------------NEFREARAVVDHLRTRHREITI------ 91 ::::::::::::::::: ::::::::::: :: :::::: d1vhqa_ 30 SRSGAQAVCFAPDKQQVDVINHLTGEAMTETRNVLIEAARITR--GE-IRPLAQADAAEL 86 d1jgta1 92 --------------------PTTELLAQLPYAVWASESVDPDIIEYLLPLTALYRAL-DG 130 ::::: ::: ::::::: : d1vhqa_ 87 DALIVPGGFGAAKNLSNFAS--------------------LGSEC-TVD-RELKALAQ-A 123 d1jgta1 131 P--E-RRILTGYGAD--------------IPLGGMHREDRLPALDTVLAHDMATFDGLNE 173 : : :::::::::: ::: ::::::::::::: d1vhqa_ 124 MHQAGKPLGFMAIAPAMLPKIFDFPLRLTIGT---------------DIDTAEVLEEMGA 168 d1jgta1 174 MS-------------PVLSTLAGHWTTHPYWDREVLDLLVSLEAGLKRRHGRDKWVLRAA 220 :: ::::::: :: :: : : ::::: d1vhqa_ 169 EHVPCPVDDIVVDED---------NKIVTTP---AY--ML-A---Q---------NIAEA 201 d1jgta1 221 M---------------ADALPAETVNRPKLSSFSRLLLDHGVAEDRVHEAKRQVVRELFD 265 : d1vhqa_ 202 ASGIDKLVSRVLVLAE-------------------------------------------- 217 d1jgta1 266 LTVGGGRHPSEVDTDDVVRSVADRT 290 d1vhqa_ 218 ------------------------- 218 HHsearch alignment (Probability: 0.02 E-value:0.13) d1jgta1 34 TPLVVLSG-----G---IDSSGVAACAHRAAGELDTVSMG 65 :::::::: : ::::::::::::::::::::::: d1vhqa_ 3 KIGVILSGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPD 42