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 <-- 0.999 --> Intermediate <-- 0.993 --> Hit

HHsearch
probability
HHsearch
probability

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1ct9a1) through the intermediate protein (d1gpma1) by significant HHsearch probability (>0.9).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1gpma1 GMP synthetase,​ central domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1ct9a1 Asparagine synthetase B,​ C-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 0.999 --> Intermediate
DALI alignment (Z-score: 17.0 Raw score:1273.10) query 1 DADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMPSK 60 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLdMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaaerg 177 :::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 116 ALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG------- 163 query 178 qtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrr 237 :::::::: d1gpma1 164 ----LPYDMLYR------------------------------------------------ 171 query 238 qyppgtkisakgfgkdrrlpitnrwregh 266 d1gpma1 172 -------------------------hpfp 175 FAST alignment (Normalized score: 13.11 Raw score:2830.00) query 1 DADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 57 ::::::::::::::::: ::::::::::::::::::::::: :::::::::: d1gpma1 1 WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCVFV 53 query 58 PSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTL 116 :::::::::::::: :::::::::::::::::::::::::: :::::::::::::::::: d1gpma1 54 DNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVEVF 112 query 117 MAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIFRL 165 :::::: ::::::::::::: :::::::::::::::: d1gpma1 113 DEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVRKI 158 query 166 AEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVK 224 ::: :::::::: d1gpma1 159 GLE------------LGLPYDMLY------------------------------------ 170 query 225 TLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 266 d1gpma1 171 ------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.53 Raw score:140.98) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 ::::::::::::::::::: :: :::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAA 174 ::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 116 ALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG---- 163 query 175 ERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTA 232 :::::::: :: d1gpma1 164 -------LPYDMLYR-HPFP---------------------------------------- 175 query 233 EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1gpma1 176 ---------------------------------- 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 4 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 63 ::::::::::::::::: ::::::::::::::::::::::::::: :::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKN-LTCVFVDNGLLR 59 query 64 DHSKGD-AAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQ 122 :::::: ::::::::::::::::::::::::::::::::: ::::::::::::::::::: d1gpma1 60 LNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGENDPEA-KRKIIGRVFVEVFDEEALK 118 query 123 EGHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPP 181 :::: :::::::::::::::::::: :::::::::::::::::::: d1gpma1 119 LEDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLELG----------- 163 query 182 IPEASITKPDYP 193 :::::::::::: d1gpma1 164 LPYDMLYRHPFP 175
Intermediate <-- 0.993 --> Hit
DALI alignment (Z-score: 9.7 Raw score:943.60) d1gpma1 1 -------------WTPAKIIDDAVARIREQVGD-DKVILGLSGGVDSSVTAMLLHRAIgk 46 :::::::::::::::::::: :::::::::::::::::::::::: d1ct9a1 1 rdwfdydavkdnvTDKNELRQALEDSVKSHLMSdVPYGVLLSGGLDSSIISAITKKYA-- 58 d1gpma1 47 nLTCVFVDNGLLRlnEAEQVLDMFGdHFGLNIVHVPAED-RFLSALA---gendPEAKRK 102 :::::::::::: :::::::::: ::::::::::::: ::::::: :::::: d1ct9a1 59 -LHSFAVGLPGSP--DLKAAQEVAN-HLGTVHHEIHFTVqEGLDAIRdviyhieTYDVTT 114 d1gpma1 103 IIGRVFVEVFDEEALKLEdVKWLAQGT-IYPD--------------------vIESAA-- 139 :::::::::::::::::: :::::::: :::: ::::: d1ct9a1 115 IRASTPMYLMSRKIKAMG-IKMVLSGEgSDEVfggylyfhkapnakelheetvRKLLAlh 173 d1gpma1 140 --------------KMGLVEPLK------------------elfKDEVRKIGLELgLPYD 167 ::::::::: ::::::::::: :::: d1ct9a1 174 mydcarankamsawGVEARVPFLdkkfldvamrinpqdkmckmeKHILRECFEAY-LPAS 232 d1gpma1 168 MLYRHPFP---------------------------------------------------- 175 :::::::: d1ct9a1 233 VAWRQKEQfsdgvgyswidtlkevaaqqvsdqqletarfrfpyntptskeaylyreifee 292 d1gpma1 176 ------------- 176 d1ct9a1 293 lfplpsaaecvpg 305 FAST alignment (Normalized score: 7.67 Raw score:1773.00) d1gpma1 1 -------------WTPAKIIDDAVARIREQV-GDDKVILGLSGGVDSSVTAMLLHRAIGK 46 :::::::::::::::::: :::::::::::::::::::::::::: d1ct9a1 1 RDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYA-- 58 d1gpma1 47 NLTCVFVDNGLLR----LNEAEQVLDMFGDHFGLNIVHVP-AEDRFLSALAGEN------ 95 :::::: :::::::: :::::::::::::: :::::::: d1ct9a1 59 -LHSFAV------GLPGSPDLKAAQ-EVANHLGTVHHEIHFTVQEGLDA-----IRDVIY 105 d1gpma1 96 ------DPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIESAA---------- 139 ::::::::::::::::::: ::::::::: d1ct9a1 106 HIETYDVTTIRASTPMYLMSRKIKA-----MGIKMVLSG-----------EGSDEVFGGY 149 d1gpma1 140 --------------------------------------KMGLVEPLKELF---------- 151 :::::::: d1ct9a1 150 LYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPF----LDKKFLDVAM 205 d1gpma1 152 ------------KDEVRKIGLELGLPYDMLYRHPFP------------------------ 175 :::::::::: :::::::::::: d1ct9a1 206 RINPQDKMCKMEKHILRECFEA-YLPASVAWRQKE-QFSDGVGYSWIDTLKEVAAQQVSD 263 d1gpma1 176 ------------------------------------------ 176 d1ct9a1 264 QQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPG 305 TMalign alignment (TM-score: 0.67 Raw score:116.75) d1gpma1 1 --------------WTPAKIIDDAVARIREQVGDD-KVILGLSGGVDSSVTAMLLHRAIG 45 ::: ::::::::::::::::: ::::::::::::::::::::::: d1ct9a1 1 RDWFDYDAVKDNVTDKN-ELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYA- 58 d1gpma1 46 KNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-----------GE 94 : ::::::::::: :::::: ::::::::::::::: ::::::: d1ct9a1 59 L--HSFAVGLPGSP--DLKAAQ-EVANHLGTVHHEIHF--TVQEGLDAIRDVIYHIET-- 109 d1gpma1 95 NDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQG-TI--YPD-----------------V 134 ::::::::::::::::::::::::: ::::: :: ::: : d1ct9a1 110 ---YDVTTIRASTPMYLMSRKIKAMGIK-MVLSGEGSDEVFGGYLYFHKAPNAKELHEET 165 d1gpma1 135 I-ESAA----------------KMGLVEPLK----E--L-------F-----KDEVRKIG 159 : :::: ::::::::: : : : :::::::: d1ct9a1 166 VRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCKMEKHILRECF 225 d1gpma1 160 LELGLPYDMLYRHPF--P------------------------------------------ 175 ::::::::::::::: : d1ct9a1 226 EAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLETARFRFPYNTPTSKEAYL 285 d1gpma1 176 -------------------- 176 d1ct9a1 286 YREIFEELFPLPSAAECVPG 305 HHsearch alignment (Probability: 0.99 E-value:0.00) d1gpma1 4 AKIIDDAVARIREQ-VGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNE 62 :::::::::::::: ::::::::::::::::::::::::: :: :::::::::: :: d1ct9a1 17 NELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKK-YA--LHSFAVGLPG---SP 70 d1gpma1 63 AEQVLDMFGDHFGLNIVHVPAED-RFLSALAGENDPE---AKRKIIGRVFVEVFDEEALK 118 ::::::::::::::::::::::: ::::::::::::: :::::::::::::::::::: d1ct9a1 71 DLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKA 130 d1gpma1 119 LEDVKWLAQGTIYPDVIESAAKMGLVEPLKELFKDEVRKI 158 ::::::::::::::::::::::::::::::::::::::: d1ct9a1 131 -MGIKMVLSGEGSDEVFGGYLYFHKAPNAKELHEETVRKL 169