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: T0582_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.971 --> Intermediate <-- 0.994 --> Hit

HHsearch
probability
HHsearch
probability

The query (T0582_Ad1.pdb) is transitively linked to the hit (d1fi2a_) through the intermediate protein (d1lrha_) by significant HHsearch probability (>0.9).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1lrha_ Auxin binding proteinRmlC-​like cupinsDouble-​stranded beta-​helixAll β
Hit d1fi2a_ GerminRmlC-​like cupinsDouble-​stranded beta-​helixAll β

Supporting Alignments

Query <-- 0.971 --> Intermediate
DALI alignment (Z-score: 9.7 Raw score:629.00) query 1 meinadftKPVVIDTDQLEWRPSPMKGVERRMLDRIG--gevARATSIVRYAPGSRFSAH 58 ::::::::::::::::::::::::::::: :::::::::::::::::: d1lrha_ 1 ---scvrdNSLVRDISQMPQSSYGIEGLSHITVAGALnhgmkEVEVWLQTISPGQRTPIH 57 query 59 THDGGEEFIVLDGVFQDE-------------HGDYPAGTYVRNPPTTSHVPGSAE---GC 102 :::::::::::::::::: :::::::::::::::::::::::: :: d1lrha_ 58 RHSCEEVFTVLKGKGTLLmgssslkypgqpqEIPFFQNTTFSIPVNDPHQVWNSDeheDL 117 query 103 TIFVKLWQ----------------------fdpadrtqfsknm 123 :::::::: d1lrha_ 118 QVLVIISRppakiflyddwsmphtaavlkfpfvwdedcfeaak 160 FAST alignment (Normalized score: 7.67 Raw score:1076.00) query 1 MEINADFTKP-------VVIDTDQLEWRPSPMKGVERRMLDRIGGEVA--------RATS 45 ::::::::::::::::::::::::: :::: d1lrha_ 1 ----------SCVRDNSLVRDISQMPQSSYGIEGLSHITVAG------ALNHGMKEVEVW 44 query 46 IVRYAPGSRFSAHTHDGGEEFIVLDGVFQDE--------------HGDYPAGTYVRNPPT 91 :::::::::::::::::::::::::::::: ::::::::::::::: d1lrha_ 45 LQTISPGQRTPIHRHSCEEVFTVLKGKGTL-LMGSSSLKYPGQPQEIPFFQNTTFSIPVN 103 query 92 TSHVPGSA----EGCTIFVKLWQFDPADRTQFSKNM------------------------ 123 ::::::: :::::::: d1lrha_ 104 DPHQVWN-SDEHEDLQVLVI----------------ISRPPAKIFLYDDWSMPHTAAVLK 146 query 124 -------------- 124 d1lrha_ 147 FPFVWDEDCFEAAK 160 TMalign alignment (TM-score: 0.67 Raw score:82.39) query 1 -MEINADFTKPVVIDTDQLEWRPSPMKGVERRMLDRIGG---EVA-RATSIVRYAPGSRF 55 :::: : : :::::::::::::::::::::::::::: : :::::::::::::: d1lrha_ 1 SCVRD-N--S-LVRDISQMPQSSYGIEGLSHITVAGALNHGM--KEVEVWLQTISPGQRT 54 query 56 SAHTHDGGEEFIVLDGVFQDE-------------HGDYPAGTYVRNPPTTSHVPGSAE-- 100 ::::::::::::::::::::: :::::::::::::::::::::::: d1lrha_ 55 PIHRHSCEEVFTVLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVNDPHQVWNSDEH 114 query 101 -GCTIFVKLWQF----------------------------------DPADRTQFSKNM 123 ::::::::::: d1lrha_ 115 EDLQVLVIISRPPAKIFLYDDWSMPHTAAVLKFPFVWDEDCFEAAK------------ 160 HHsearch alignment (Probability: 0.97 E-value:0.00) query 10 PVVIDTDQLEWRPSPMKGVERRML--DRIGGEVARATSIVRYAPGSRFSAHTHDGGEEFI 67 :::::::::::::::::::::::: :::::::::::::::::::::::::::::::::: d1lrha_ 7 SLVRDISQMPQSSYGIEGLSHITVAGALNHGMKEVEVWLQTISPGQRTPIHRHSCEEVFT 66 query 68 VLDGVFQDEHGD-------------YPAGTYVRNPPTTSHVP--GSA-EGCTIFV 106 :::::::::::: ::::::::::::::::: ::: ::::::: d1lrha_ 67 VLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVNDPHQVWNSDEHEDLQVLV 121
Intermediate <-- 0.994 --> Hit
DALI alignment (Z-score: 11.5 Raw score:832.70) d1lrha_ 1 -----------------------------scvrdNSLVRDIsqMPQSS-yGIEGLSHITV 30 ::::::: ::::: :::::::::: d1fi2a_ 1 tdpdplqdfcvadldgkavsvnghtckpmseagdDFLFSSK-lTKAGNtsTPNGSAVTEL 59 d1lrha_ 31 aGALN-HGMK--EVEVWLQTISPGQRTPIHRHS-CEEVFTVLKGKGTLLMGSSSLKYpGQ 86 :::: :::: ::::::::::::::::::::: ::::::::::::::::::::::: :: d1fi2a_ 60 -DVAEwPGTNtlGVSMNRVDFAPGGTNPPHIHPrATEIGMVMKGELLVGILGSLDSG-NK 117 d1lrha_ 87 PQEIPFFQNTTFSIPVNDPHQVWNSDEhEDLQVLVIISRPPAKIFLYD-----------d 135 ::::::::::::::::::::::::::: :::::::::::::::::::: d1fi2a_ 118 LYSRVVRAGETFVIPRGLMHFQFNVGK-TEAYMVVSFNSQNPGIVFVPltlfgsdppipt 176 d1lrha_ 136 wsmphtaavlkfpfvwdedcfeaak 160 d1fi2a_ 177 pvltkalrveagvvellkskfaggs 201 FAST alignment (Normalized score: 9.01 Raw score:1616.00) d1lrha_ 1 SCVRDN-----------------------------------SLVRDISQMPQSSYGI--- 22 :::: d1fi2a_ 1 ------TDPDPLQDFCVADLDGKAVSVNGHTCKPMSEAGDDFLFS------------SKL 42 d1lrha_ 23 ---------EGLSHITVAGALN-HGM--KEVEVWLQTISPGQRTPIHRH-SCEEVFTVLK 69 ::::::: ::::: ::: ::::::::::::::::::::: :::::::::: d1fi2a_ 43 TKAGNTSTPNGSAVTE-LDVAEWPGTNTLGVSMNRVDFAPGGTNPPHIHPRATEIGMVMK 101 d1lrha_ 70 GKGTLLMGSSSLKYP----GQPQEIPFFQNTTFSIPVNDPHQVWNSDEHEDLQVLVIISR 125 :::::::::: :::::::::::::::::::::::::::: :::::::::::: d1fi2a_ 102 GELLVGILGS-----LDSGNKLYSRVVRAGETFVIPRGLMHFQFNVG-KTEAYMVVSFNS 155 d1lrha_ 126 PPAKIFLYDDWSMPHTAAVLKFPFVWDEDCFEAAK------------------------- 160 ::::::: d1fi2a_ 156 QNPGIVF----------------------------VPLTLFGSDPPIPTPVLTKALRVEA 187 d1lrha_ 161 -------------- 161 d1fi2a_ 188 GVVELLKSKFAGGS 201 TMalign alignment (TM-score: 0.65 Raw score:104.57) d1lrha_ 1 -------------SCVR----------------DN-SL-VRDISQMPQSSYGIEGLSHIT 29 :: :: :: ::::::::::::::::::::: d1fi2a_ 1 TDPDPLQDFCVAD--LDGKAVSVNGHTCKPMSEAGDDFLFSSKLTKAGNTSTPNGSAVTE 58 d1lrha_ 30 VAGALNHG-MK--EVEVWLQTISPGQRTPIHRH-SCEEVFTVLKGKGTLLMGSSSLKYPG 85 ::::::: :: :::::::::::::::::::: :::::::::::::::::::::::::: d1fi2a_ 59 -LDVAEWPGTNTLGVSMNRVDFAPGGTNPPHIHPRATEIGMVMKGELLVGILGSLDSGNK 117 d1lrha_ 86 QPQEIPFFQNTTFSIPVNDPHQVWNSDEHEDLQVLVIISRPPAKIFLYDDWSMPHTAAV- 144 :::::::::::::::::::::::::: :::::::::::::::::::::: ::: d1fi2a_ 118 -LYSRVVRAGETFVIPRGLMHFQFNVG-KTEAYMVVSFNSQNPGIVFVPL------TLFG 169 d1lrha_ 145 LK-------------------------------FPFVWDEDCFEAAK 160 : d1fi2a_ 170 -SDPPIPTPVLTKALRVEAGVVELLKSKFAGGS-------------- 201 HHsearch alignment (Probability: 0.99 E-value:0.00) d1lrha_ 6 NSLVRDISQMPQSSYGIEGLSHITVAGALNHGMKEVEVW--LQTISPGQRTPIHRHS-CE 62 ::::::::::::::::::::::::::::::::::::::: :::::::::::::::: :: d1fi2a_ 35 DFLFSSKLTKAGNTSTPNGSAVTELDVAEWPGTNTLGVSMNRVDFAPGGTNPPHIHPRAT 94 d1lrha_ 63 EVFTVLKGKGTLLMGSSSLKYPGQPQEIPFFQNTTFSIPVNDPHQVWNSDEHEDLQVLVI 122 :::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::: d1fi2a_ 95 EIGMVMKGELLVGILGSLDS-GNKLYSRVVRAGETFVIPRGLMHFQFNVGKTEAYMVVSF 153 d1lrha_ 123 ISRPPAKIFLYDDWS 137 ::::::::::::::: d1fi2a_ 154 NSQNPGIVFVPLTLF 168