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 <-- 1.868 --> Intermediate <-- 1.395 --> Hit

SVM
score
SVM
score

The query (T0582_Ad1.pdb) is transitively linked to the hit (d1pf0a_) through the intermediate protein (d1sfna_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1sfna_ Hypothetical protein DR1152RmlC-​like cupinsDouble-​stranded beta-​helixAll β
Hit d1pf0a_ Putative ion channel CnbDcAMP-​binding domain-​likeDouble-​stranded beta-​helixAll β

Supporting Alignments

Query <-- 1.868 --> Intermediate
DALI alignment (Z-score: 10.4 Raw score:726.80) query 1 -----meinadfTKPVVIDTDQLEWRPSP-MKGVERRMLDRIG--gevARATSIVRYAPG 52 ::::::::::::::::: ::::::::::::: :::::::::::: d1sfna_ 1 mkhlgqtrsalhGSHAVITPETFVRTALAeWPGSAIVLHIAPVvglgaRFVQFTAEMPAG 60 query 53 SRfsaHTHDGGEEFIVLDGVFQDE----HGDYPAGTYVRNPPTTSHVPGSAEGCTIFVKL 108 :: ::::::::::::::::::: :::::::::::::::::::::::::::::::: d1sfna_ 61 AQ--aTESVYQRFAFVLSGEVDVAvggeTRTLREYDYVYLPAGEKHMLTAKTDARVSVFE 118 query 109 WqFDPA-----DRTQFSKNM---------------------------------------- 123 : :::: ::::::::: d1sfna_ 119 K-PYQTvegvqAPGVYWGNErenpgypfegddhliarkllpdepafdfmvstmsfapgas 177 query 124 ------------------------------------------------------------ 124 d1sfna_ 178 lpyaevhymehgllmlegeglykleenyypvtagdiiwmgahcpqwygalgrnwskylly 237 query 124 -------- 124 d1sfna_ 238 kdmnrhpl 245 FAST alignment (Normalized score: 7.10 Raw score:1232.00) query 1 MEINADF------------TKPVVIDTDQLEWRPS-PMKGVERRMLDRIGGEVA------ 41 :::::::::::::::: ::::::::::: d1sfna_ 1 -------MKHLGQTRSALHGSHAVITPETFVRTALAEWPGSAIVLHI-------APVVGL 46 query 42 ---RATSIVRYAPGSRFSAHTHDGGEEFIVLDGVFQDE-----HGDYPAGTYVRNPPTTS 93 :::::::::::::::: :::::::::::::::: ::::::::::::::::: d1sfna_ 47 GARFVQFTAEMPAGAQATE--SVYQRFAFVLSGEVDV-AVGGETRTLREYDYVYLPAGEK 103 query 94 HVPGSAEGCTIFVKLWQFDP----------ADRTQFSKNM-------------------- 123 :::::::::::::: :::::::: d1sfna_ 104 HMLTAKTDARVSVF------EKPYQTVEGVQAPGVYWG--NERENPGYPFEGDDHLIARK 155 query 124 ------------------------------------------------------------ 124 d1sfna_ 156 LLPDEPAFDFMVSTMSFAPGASLPYAEVHYMEHGLLMLEGEGLYKLEENYYPVTAGDIIW 215 query 124 ------------------------------ 124 d1sfna_ 216 MGAHCPQWYGALGRNWSKYLLYKDMNRHPL 245 TMalign alignment (TM-score: 0.75 Raw score:91.78) query 1 ----------MEINADFTKPVVIDTDQ-LEWRPSP-MKGVERRMLDRIG-----GEVARA 43 ::::::::: :: ::::::: ::::::::::::: ::: d1sfna_ 1 MKHLGQTRSA-----LHGSHAVIT-PETFVRTALAEWPGSAIVLHIAPVVGLGA---RFV 51 query 44 TSIVRYAPGSRFSAHTHDGGEEFIVLDGVFQDE----HGDYPAGTYVRNPPTTSHVPGSA 99 :::::::::::: :: ::::::::::::::::: ::::::::::::::::::::::: d1sfna_ 52 QFTAEMPAGAQA-TE-SVYQRFAFVLSGEVDVAVGGETRTLREYDYVYLPAGEKHMLTAK 109 query 100 EGCTIFVKLWQFDP----ADRTQFSKNM-------------------------------- 123 :::::::::::::: :::::::::: d1sfna_ 110 TDARVSVFEKPYQTVEGVQAPGVYWGNERENPGYPFEGDDHLIARKLLPDEPAFDFMVST 169 query 124 ------------------------------------------------------------ 124 d1sfna_ 170 MSFAPGASLPYAEVHYMEHGLLMLEGEGLYKLEENYYPVTAGDIIWMGAHCPQWYGALGR 229 query 124 ---------------- 124 d1sfna_ 230 NWSKYLLYKDMNRHPL 245 HHsearch alignment (Probability: 0.96 E-value:0.00) query 11 VVIDTDQLEWRPSPM-KGVERRMLDRI--GGEVARATSIVRYAPGSRFSAHTHDGGEEFI 67 ::::::::::::::: ::::::::::: ::::::::::::::::::::::::: :::: d1sfna_ 16 AVITPETFVRTALAEWPGSAIVLHIAPVVGLGARFVQFTAEMPAGAQATESVYQ--RFAF 73 query 68 VLDGVFQ----DEHGDYPAGTYVRNPPTTSHVPGSAEGCTIFVKLWQFDPAD 115 ::::::: ::::::::::::::::::::::::::::::::::::::::: d1sfna_ 74 VLSGEVDVAVGGETRTLREYDYVYLPAGEKHMLTAKTDARVSVFEKPYQTVE 125
Intermediate <-- 1.395 --> Hit
DALI alignment (Z-score: 5.8 Raw score:377.30) d1sfna_ 1 mkhlgqtrsalhgshavitpetfvrtalaewpgsaivLHIApvvglgarfvQFTAEMPAG 60 :::: ::::::::: d1pf0a_ 1 --------vrrgdfvrnwqlvaavplfqklgpavlveIVRA----------LRARTVPAG 42 d1sfna_ 61 AQATE--SVYQRFAFVLSGEVDVAVgGETRTLREYDYV-YLPA----GEKHMLTAKTDAR 113 ::::: :::::::::::::::::: :::::::::::: :::: ::::::::::::: d1pf0a_ 43 AVICRigEPGDRMFFVVEGSVSVAT-PNPVELGPGAFFgEMALisgePRSATVSAATTVS 101 d1sfna_ 114 VSVFEKPyqtvegvqapgvywgnerenPGypfegddhliaRK--LLPDepafdfmvstms 171 ::::::: :: :: :::: d1pf0a_ 102 LLSLHSA------------dfqmlcssSP-----------EIaeIFRK------------ 126 d1sfna_ 172 fapgaslpyaevhymehgllmlegeglykleenyypvtagdiiwmgahcpqwygalgrnw 231 d1pf0a_ 127 ------------------------------------------------------------ 127 d1sfna_ 232 skyllykdmnrhpl 245 d1pf0a_ 127 -------talerrg 133 FAST alignment (Normalized score: 3.38 Raw score:609.20) d1sfna_ 1 MKHLGQTRSALHGSHAVITPETFVRTALAEWPGSAIVLHIAPVVGLGARF---------- 50 d1pf0a_ 1 --------------------------------------------------VRRGDFVRNW 10 d1sfna_ 51 ----------------------VQFTAEMPAGAQATES------VYQRFAFVLSGEVDVA 82 :::::::::::: :::::::::::::::: d1pf0a_ 11 QLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAV----ICRIGEPGDRMFFVVEGSVSVA 66 d1sfna_ 83 VGGETRTLREYDYVYLP---------AGEKHMLTAKTDARVSVFEKPYQTVEGVQAPGVY 133 : ::::::::::: :::::::::::::::::: d1pf0a_ 67 T-PNPVELGPGAF----FGEMALISGEPRSATVSAATTVSLLSL---------------- 105 d1sfna_ 134 WGNERENPGYPFEGDDHLIARKLLPDEPAFDFMVSTMSFAPGASLPYAEVHYMEHGLLML 193 d1pf0a_ 106 ------------------------------------------------------------ 106 d1sfna_ 194 EGEGLYKLEENYYPVTAGDIIWMGAHCPQWYGALGRNWSKYLLYKDMNRHPL-------- 245 d1pf0a_ 106 ----------------------------------------------------HSADFQML 113 d1sfna_ 246 -------------------- 246 d1pf0a_ 114 CSSSPEIAEIFRKTALERRG 133 TMalign alignment (TM-score: 0.28 Raw score:68.90) d1sfna_ 1 ----------------MKHLGQTRSALHGSHAVITPETFVRTALAEWPGSAIVLHIAPVV 44 : d1pf0a_ 1 VRRGDFVRNWQLVAAV------------------------------------P------- 17 d1sfna_ 45 GLGARFVQFTAEMPAGAQATES-VYQRFAFVLSGEVDVAVGGETRTLREYDYVYLPAGEK 103 ::::: :::: :::: : d1pf0a_ 18 --------LFQKL-----GPAVL--VEIV------------------------R------ 32 d1sfna_ 104 HMLTAKTDARVSVFEKPYQTVEGVQAPGVYWGNERENPGYPFEGDDHLIARKLLPDEPAF 163 d1pf0a_ 33 ------------------------------------------------------------ 33 d1sfna_ 164 DFMVSTMSFAPGASLPYAEVHYMEHGLLMLEGEGLYKLEENYYPVTAGDII-WM--G-AH 219 ::::::::::::::::::::: :::::::::::::: :::::::::::: :: : :: d1pf0a_ 33 --ALRARTVPAGAVICRIGEPGD-RMFFVVEGSVSVAT-PNPVELGPGAFFGEMALISGE 88 d1sfna_ 220 CP-QWYGALGRNWSKYLLYKDM-------------------------NRHPL 245 :: ::::::: :::::::::: d1pf0a_ 89 PRSATVSAAT--TVSLLSLHSADFQMLCSSSPEIAEIFRKTALERRG----- 133 HHsearch alignment (Probability: 0.70 E-value:0.00) d1sfna_ 65 ESVYQRFAFVLSGEVDVAVGGETRTLREYDYVY-----LPAGEKHMLTAKTDARVSVFEK 119 ::::::::::::::::::::: ::::::::::: :::::::::::::::::::::: d1pf0a_ 49 GEPGDRMFFVVEGSVSVATPN-PVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHS 107