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 <-- 1.890 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1nrwa_) 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 d1nrwa_ Hypothetical protein YwpJHAD-​likeHAD-​likeα/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 <-- 1.890 --> Hit
DALI alignment (Z-score: 12.5 Raw score:952.80) d1nnla_ 1 selrklfysADAVCFDVDSTVIREegidelakicgvedavpfkaalterlaliqpsreqv 60 ::::::::::::::: d1nrwa_ 1 ---------MKLIAIDLDGTLLNS------------------------------------ 15 d1nnla_ 61 qrliaeqpPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVAS--KLNIpatNVFANr 118 ::::::::::::::::::::::::::::::::::::: :::: ::::: d1nrwa_ 16 -------kHQVSLENENALRQAQRDGIEVVVSTGRAHFDVMSIFEplGIKT---WVISAn 65 d1nnla_ 119 lkfyfngeyagfdET--------------------------------------------- 133 :: d1nrwa_ 66 gavihdpegrlyhHEtidkkraydilswlesenyyyevftgsaiytpqngrelldveldr 125 d1nnla_ 134 ------------------------------------------------------------ 134 d1nrwa_ 126 frsanpeadlsvlkqaaevqysqsgfayinsfqelfeadepidfynilgfsffkekleag 185 d1nnla_ 134 -------------------------QPtaesgGKGKVIKLLKEKFHFK--KIIMIGDGAT 166 :: :::::::::::::::: :::::::::: d1nrwa_ 186 wkryehaedltlvssaehnfelssrKA-----SKGQALKRLAKQLNIPleETAAVGDSLN 240 d1nnla_ 167 DMEACPPADAFIGFGgnVIRQQVKDNAKWYITD------FVELLG-- 205 ::::::::::::::: :::::::::::::::: :::::: d1nrwa_ 241 DKSMLEAAGKGVAMG--NAREDIKSIADAVTLTndehgvAHMMKHll 285 FAST alignment (Normalized score: 7.11 Raw score:1718.00) d1nnla_ 1 SELRKLFYSA-DAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSREQ 59 :::::::::::: d1nrwa_ 1 ----------MKLIAIDLDGTLL------------------------------------- 13 d1nnla_ 60 VQRLIAEQP---PHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVAS--KLNIPATNV 114 ::::::::::::::::::::::::::::::::::::: :::: d1nrwa_ 14 ---------NSKHQVSLENENALRQAQRDGIEVVVSTGRAHFDVMSIFEPLGIKT----- 59 d1nnla_ 115 FANRLKFYFNGEYAG--------------------------------------------- 129 d1nrwa_ 60 ---------------WVISANGAVIHDPEGRLYHHETIDKKRAYDILSWLESENYYYEVF 104 d1nnla_ 130 ------------------------------------------------------------ 130 d1nrwa_ 105 TGSAIYTPQNGRELLDVELDRFRSANPEADLSVLKQAAEVQYSQSGFAYINSFQELFEAD 164 d1nnla_ 130 -------------------------------------------FDETQPTAESGGKGKVI 146 ::::: :::::: d1nrwa_ 165 EPIDFYNILGFSFFKEKLEAGWKRYEHAEDLTLVSSAEHNFELSSRKA------SKGQAL 218 d1nnla_ 147 KLLKEKFHF--KKIIMIGDGATDMEACPPADAFIGFGG-NVIRQQVKDNAKWYIT----- 198 ::::::::: :::::::::::::::::::::::: :::::::::::::: d1nrwa_ 219 KRLAKQLNIPLEETAAVGDSLNDKSMLEAAGKGVA---MGNAREDIKSIADAV--TLTND 273 d1nnla_ 199 --DFVELLG---- 205 :::::: d1nrwa_ 274 EHGVAHMM-KHLL 285 TMalign alignment (TM-score: 0.60 Raw score:122.10) d1nnla_ 1 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSREQV 60 ::::::::::::::: d1nrwa_ 1 ---------MKLIAIDLDGTLLNS------------------------------------ 15 d1nnla_ 61 QRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVAS-KLNIPATNVFAN-- 117 :::::::::::::::::::::::::::::::::::::: ::::: ::::: d1nrwa_ 16 -------KHQVSLENENALRQAQRDGIEVVVSTGRAHFDVMSIFEPLGIKT--WVISANG 66 d1nnla_ 118 -------------------------------------RL-KF-Y---------------- 122 :: :: : d1nrwa_ 67 AVIHDPEGRLYHHETIDKKRAYDILSWLESENYYYEVFTGSAIYTPQNGRELLDVELDRF 126 d1nnla_ 123 -------------------------FNGEY----AG------FDETQ------------- 134 ::: :: ::::: d1nrwa_ 127 RSANPEADLSVLKQAAEVQYSQSGF--AYINSFQELFEADEPIDFYNILGFSFFKEKLEA 184 d1nnla_ 135 -----------P----------TAES-GGKGKVIKLLKEKFHFK--KIIMIGDGATDMEA 170 : :::: ::::::::::::::::: :::::::::::::: d1nrwa_ 185 GWKRYEHAEDLTLVSSAEHNFELSSRKASKGQALKRLAKQLNIPLEETAAVGDSLNDKSM 244 d1nnla_ 171 CPPADAFIGFGGNVIRQQVKDNAKWYIT-----DFVEL-LG-- 205 ::::::::::: ::::::::::::::: ::::: :: d1nrwa_ 245 LEAAGKGVAMG--NAREDIKSIADAVTLTNDEHGVAHMMKHLL 285 HHsearch alignment (Probability: 1.00 E-value:0.00) d1nnla_ 140 GGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITD 199 :::::::::::::::::::::::::::::::::::::::::: :::::::::::::::: d1nrwa_ 214 KGQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAGKGVAMG--NAREDIKSIADAVTLT 271 d1nnla_ 200 FV 201 :: d1nrwa_ 272 ND 273