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 <-- 0.606 --> Intermediate <-- 1.046 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1d4oa_) through the intermediate protein (d1nnla_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1nnla_ Phosphoserine phosphataseHAD-​likeHAD-​likeα/β
Hit d1d4oa_ Transhydrogenase domain III (dIII)DHS-​like NAD/​FAD-​binding domainDHS-​like NAD/​FAD-​binding domainα/β

Supporting Alignments

Query <-- 0.606 --> Intermediate
DALI alignment (Z-score: 3.0 Raw score:421.70) query 1 dadeevysalvvglrAYVAknGFRSVLIGLSggiDSAL---------------------- 38 :::: :::::::::: :::: d1nnla_ 1 -----------selrKLFY--SADAVCFDVD---STVIreegidelakicgvedavpfka 44 query 39 -----------------------------vaAIACDALG--aqNVYGVSMPskyssdhSK 67 :::::::: :::::::: :: d1nnla_ 45 alterlaliqpsreqvqrliaeqpphltpgiRELVSRLQernvQVFLISGG-------FR 97 query 68 GDAAELARRTGL---NFRT------------------VSIEpmfdaymaslgltglaeen 106 :::::::::::: :::: :::: d1nnla_ 98 SIVEHVASKLNIpatNVFAnrlkfyfngeyagfdetqPTAE------------------- 138 query 107 lqsRLRGTTLMAISNQE----GHIVLAPGnkselavgystlyGDSV------gAYGPiKD 156 :::::::::::::: :::::::: :::: :::: :: d1nnla_ 139 ---SGGKGKVIKLLKEKfhfkKIIMIGDG------------aTDMEacppadaFIGF-GG 182 query 157 VYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaag 216 :: d1nnla_ 183 NV---------------------------------------------------------- 184 query 217 ydrelvvktlrmvdtaeykRRQY-PPGTkisakgfgkdrrlpitnrwregh 266 :::: :::: d1nnla_ 185 --------------irqqvKDNAkWYIT----------------dfvellg 205 FAST alignment (Normalized score: 1.83 Raw score:427.80) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGI-DSALVAAIACDALGAQN-VYGVSMP 58 :::::::: :::::: d1nnla_ 1 ----------------------------------SELRKLFYS---------ADAVCFD- 16 query 59 S----------------------------------------------------KYSSDHS 66 ::::::: d1nnla_ 17 -VDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGI 75 query 67 KGDAAELARRTGLNFRTVSIE--------------------------------------- 87 :::::::: ::::::::::: d1nnla_ 76 RELVSRLQ-ERNVQVFLISG-GFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDET 133 query 88 PMFDAYMASLGLTGLAEENLQS--RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLY 144 :::: :::::::::::::::: :::: d1nnla_ 134 QPTA------------------ESGGKGKVIKLLKEKFHFKKIIM--------------- 160 query 145 ---------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 195 :::::::: d1nnla_ 161 IGDGATDMEACPPADAF------------------------------------------- 177 query 196 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 255 d1nnla_ 178 ------------------------------------------------------------ 178 query 256 LPITNRWREGH---------------------------- 266 d1nnla_ 178 -----------IGFGGNVIRQQVKDNAKWYITDFVELLG 205 TMalign alignment (TM-score: 0.36 Raw score:94.46) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSA----------------------- 37 :::::::: : :::::::: ::::: d1nnla_ 1 -----------SELRKLFY-S-ADAVCFDV--DSTVIREEGIDELAKICGVEDAVPFKAA 45 query 38 --------------------------L-VAAIACDALGA-QNVYGVSMPSKYSSDHSKGD 69 : ::::::::::: ::::::::: : :::: d1nnla_ 46 LTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISG---G---FRSI 99 query 70 AAELARRTGLNFR-TV-S-------------IEPMF-DAYMASLGLTGLAEENLQSRLRG 113 ::::::::::::: :: : ::::: ::::::: d1nnla_ 100 VEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPT----------------AESGGKG 143 query 114 TTLMAISNQE-G-HIVLAPGNKSELAVGYSTLYGDSVG----AYGPIKDVYKTSIFRLAE 167 :::::::::: : ::::::: : : :::::: :::::: ::: d1nnla_ 144 KVIKLLKEKFHFKKIIMIGD---G------A-TDMEACPPADAFIGFG-GNV-------- 184 query 168 WRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLR 227 : : d1nnla_ 185 ----------------------------I--R---------------------------- 186 query 228 MVDTAEYKRRQYPPGTKI------SAKGFGKDRRLPITNRWREGH 266 : :: ::: ::::::: d1nnla_ 187 -Q--QV-KDN-AKWYITDFVELLG--------------------- 205 HHsearch alignment (Probability: 0.01 E-value:0.18) query 144 YGDSVGAYGPIK 155 :::::::::::: d1nnla_ 161 IGDGATDMEACP 172
Intermediate <-- 1.046 --> Hit
DALI alignment (Z-score: 7.2 Raw score:660.70) d1nnla_ 1 --------SELRKLFYSADAVCFDVDSTVIREegidelakicgvedavpfkaalterlal 52 :::::::::::::::::::::::: d1d4oa_ 1 gthteinlDNAIDMIREANSIIITPGYGLCAA---------------------------- 32 d1nnla_ 53 iqpsreqvqrliaeqppHLTPGIRELVSRLQERNVQVFLISGGF----rSIVEHVASKLN 108 ::::::::::::::::::::::::::: ::::::::::: d1d4oa_ 33 -----------------KAQYPIADLVKMLSEQGKKVRFGIHPVagrmpGQLNVLLAEAG 75 d1nnla_ 109 IPATNVFAnrlkfyfngeyagfdetqptaesGGKGKVIKllkekfhfkkIIMIG--DGAT 166 :::::::: :::::::: ::::: :::: d1d4oa_ 76 VPYDIVLE----------------------mDEINHDFP--------dtDLVLVigANDT 105 d1nnla_ 167 D-----------------mEACPpADAFIGFGgnVIRQ--------QVKDN-aKWYIT-- 198 : :::: :::::::: :::: ::::: ::::: d1d4oa_ 106 VnsaaqedpnsiiagmpvlEVWK-SKQVIVMK--RSLGvgyaavdnPIFYKpnTAMLLgd 162 d1nnla_ 199 ---DFVELLG----- 205 ::::::: d1d4oa_ 163 akkTCDALQAkvres 177 FAST alignment (Normalized score: 4.99 Raw score:950.10) d1nnla_ 1 S---------ELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLA 51 :::::::::::::::: d1d4oa_ 1 -GTHTEINLDNAIDMIREANSIIITP---------------------------------- 25 d1nnla_ 52 LIQPSREQVQRLIAEQPPHL---------TPGIRELVSRLQERNVQVFLISGGFR----- 97 :::::::::::::::::::::: d1d4oa_ 26 --------------------GYGLCAAKAQYPIADLVKMLSEQGKKVRFGI----HPVAG 61 d1nnla_ 98 ---SIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAES---GGKGKVIKLLKE 151 ::::::::::::::::: ::::::::: d1d4oa_ 62 RMPGQLNVLLAEAGVPYDIV-------------------------LEMDEINHDFPD--- 93 d1nnla_ 152 KFHFKKIIMIG--------DGATDMEA-------------------CPPADAFIGFGGNV 184 ::::: ::::::::: d1d4oa_ 94 -----------TDLVLVIGANDTV---NSAAQEDPNSIIAGMPVLEVWKSKQVIV----- 134 d1nnla_ 185 IR-------------QQVKDNA----KWYIT------DFVELLG------ 205 :::: :::: :::::: d1d4oa_ 135 --MKRSLGVGYAAVDNPIF---YKPNTAML-LGDAKKTCDALQ-AKVRES 177 TMalign alignment (TM-score: 0.47 Raw score:96.72) d1nnla_ 1 --------SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLAL 52 :::::::::::::::::::::::: d1d4oa_ 1 GTHTEINLDNAIDMIREANSIIITPGYGLCAA---------------------------- 32 d1nnla_ 53 IQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNV-QVFLISGGF---RSIVEHVAS-KL 107 :::::::::::::::::: ::::::::: ::::::::: :: d1d4oa_ 33 -----------------KAQYPIADLVKMLSEQGKKVRFGIHPVAGRMPGQLNVLLAEAG 75 d1nnla_ 108 NIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGD-GAT 166 ::::::::: : ::: :::: ::::::::: ::: d1d4oa_ 76 VPYDIVLEM------------------D--------EIN-HDFP---DTDLVLVIGANDT 105 d1nnla_ 167 DME----------------ACPPADAFIGFGGNVIRQ------QV-KDN---AKWYIT-- 198 ::: :::::::::::: :::: :: ::: :::::: d1d4oa_ 106 VNSAAQEDPNSIIAGMPVLEVWKSKQVIVMK--RSLGVGYAAVDNPIFYKPNTAMLLGDA 163 d1nnla_ 199 --DFVELL-G---- 205 :::::: : d1d4oa_ 164 KKTCDALQAKVRES 177 HHsearch alignment (Probability: 0.01 E-value:0.19) d1nnla_ 72 TPGIRELVSRLQERNVQVFLI----SGGFRSIVEHVASKLNIPATN 113 ::::::::::::::::::::: ::::::::::::::::::::: d1d4oa_ 35 QYPIADLVKMLSEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDI 80