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: T592_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.610 --> Intermediate <-- 1.257 --> Hit

SVM
score
SVM
score

The query (T592_B.pdb B) is transitively linked to the hit (d1vdra_) through the intermediate protein (d1t6t1_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1t6t1_ Hypothetical protein aq 2086Toprim domain (Pfam 01751)Toprim domain (Pfam 01751)α/β
Hit d1vdra_ Dihydrofolate reductase,​ prokaryotic typeDihydrofolate reductasesDihydrofolate reductasesα/β

Supporting Alignments

Query <-- 0.610 --> Intermediate
DALI alignment (Z-score: 4.8 Raw score:306.10) query 1 npneayrhymkklsyetDIADLSIDikkgyEGIIVVDvRDAEaYKECH----IPTAISIP 56 :::::::: ::::::: :::: ::::: :::::::: d1t6t1_ 1 -----------prnlseWIKELKKA----sREAVILV-EGKN-DKKALskfsIKNVIDLS 43 query 57 gnKINEdTTKRLSKEK-VIITYCWGPA--CNGATKAAAKFAQLGFRVKE------liggi 107 :::: ::::::::: :::::::::: :::::::::::::::::::: d1t6t1_ 44 gkRYAD-VVDMLEGKWeKVILLFDLDThgERINQKMKELLSSQGFLVDEnfrnflkkwni 102 query 108 EYWRkengevegtlgakadlfwnmkkesle 137 :::: d1t6t1_ 103 IHIE------------------------ei 108 FAST alignment (Normalized score: 4.56 Raw score:554.40) query 1 NPNEAYRHYMKKLSYET------DIADLSIDIKKGYEGIIVVDVRDAEAYKECH------ 48 ::::::::: ::::::: ::::::: d1t6t1_ 1 -----------------PRNLSEWIKELKKAS----REAVILV-EGKNDKK---ALSKFS 35 query 49 IPTAISIPGNKI-----NEDTTKRLSKE--KVIITYCWGPA---CNGATKAAAKFAQLGF 98 :::::: ::::::: ::: :::::::::: :::::::::::::::: d1t6t1_ 36 IKNVID------LSGKRYADVVDM-LEGKWEKVILLFDLD-THGERINQKMKELLSSQGF 87 query 99 RVKELIGGIEYWRKENGEVEGTLGAKADLFWNMKKESLE------------------ 137 ::: d1t6t1_ 88 LVD------------------------------------ENFRNFLKKWNIIHIEEI 108 TMalign alignment (TM-score: 0.48 Raw score:65.09) query 1 --NPNEAYRHYMKKLSYETDIA-DLS-IDIKKGYEGIIVVDVRDAEAYKECHI--P---- 50 :: ::: ::: :::::::::: : :: ::: : d1t6t1_ 1 PR------------------NLSEWIKELK-KASREAVILV-E----GK-NDKKALSKFS 35 query 51 -T-AISIPGNKINEDTTKRL--SKEKVIITYCWGPA--CNGATKAAAKFAQLGFRVKE-- 102 : :::::::::: :::::: ::: :::::::::: :::::::::::::::::::: d1t6t1_ 36 IKNVIDLSGKRYA-DVVDMLEGKWE-KVILLFDLDTHGERINQKMKELLSSQGFLVDENF 93 query 103 LI-GG---IEYWRKENGEVEGTLGAKADLFWNMKKESLE 137 :: :: :::::: : d1t6t1_ 94 RNFLKKWNIIHIEE--I---------------------- 108 HHsearch alignment (Probability: 0.05 E-value:0.04) query 49 IPTAISIPGNKINEDTTKRLSKEKVIITYCWGPACNGATKAAA----KFAQLGFRV 100 ::::::::::::::::::::::::::::::::: :::::::: ::::::::: d1t6t1_ 36 IKNVIDLSGKRYADVVDMLEGKWEKVILLFDLD--THGERINQKMKELLSSQGFLV 89
Intermediate <-- 1.257 --> Hit
DALI alignment (Z-score: 4.7 Raw score:340.50) d1t6t1_ 1 ---------------------pRNLSEWIKELKKASREAVILVEGkNDKKALSKfSIKN- 38 ::::::::::::::::::::::: :::::::: :::: d1vdra_ 1 elvsvaalaenrvigrdgelpwPSIPADKKQYRSRIADDPVVLGR-TTFESMRD-DLPGs 58 d1t6t1_ 39 -VIDLSG-------------KRYADVVDMLEG-KWEKVILLFdldthGERINQKMKELLS 83 :::::: :::::::::::: ::::::::: ::::::::::::: d1vdra_ 59 aQIVMSRsersfsvdtahraASVEEAVDIAASlDAETAYVIG-----GAAIYALFQPHLD 113 d1t6t1_ 84 sqgflvDENFrnflKKWN-----------------------------iihieei 108 :::: :::: d1vdra_ 114 ------RMVL----SRVPgeyegdtyypewdaaeweldaetdhegftlqewvrs 157 FAST alignment (Normalized score: 4.78 Raw score:622.50) d1t6t1_ 1 PRN------------------------LSEWIKELKKASREAVILVEGKNDKKALSKFSI 36 ::::::::::::::::::: :::::::::::: d1vdra_ 1 ---ELVSVAALAENRVIGRDGELPWPSIPADKKQYRSRIADDPVVL-GRTTFESMRDDL- 55 d1t6t1_ 37 K---NVIDLSG---------------KRYADVVDMLEG--KWEKVILLFDLDTHGERINQ 76 ::::: ::::::::::: ::::::::: :::::: d1vdra_ 56 -PGSAQIVM--SRSERSFSVDTAHRAASVEEAVDIAA-SLDAETAYVIG-----GAAIYA 106 d1t6t1_ 77 KMKELLSSQG-FLVDENFRNFLKKWNIIHIEEI--------------------------- 108 ::::: :::: d1vdra_ 107 LFQPH-----LDRMV------------------LSRVPGEYEGDTYYPEWDAAEWELDAE 143 d1t6t1_ 109 -------------- 109 d1vdra_ 144 TDHEGFTLQEWVRS 157 TMalign alignment (TM-score: 0.56 Raw score:60.95) d1t6t1_ 1 -----------------------PRNLSEWIKELKKASREAVILVEGKNDKKALSKFSIK 37 :: :::::::::::::::::: :::::::::::::: d1vdra_ 1 ELVSVAALAENRVIGRDGELPWP-SI-PADKKQYRSRIADDPVVL-GRTTFESMRDDLPG 57 d1t6t1_ 38 -NVIDLSG-------------KRYADVVDMLEG-KWEKVILLFDLDTHGERINQKMKELL 82 ::::::: :::::::::::: ::::::::::: :::::::::: d1vdra_ 58 SAQIVMSRSERSFSVDTAHRAASVEEAVDIAASLDAETAYVIGGA--AIYALFQPHL--- 112 d1t6t1_ 83 SSQGFLVDENFRNFLKKW---N-I-IH----------------------------IEEI 108 :::: :: :: : : :: d1vdra_ 113 ------DRMV--LS--RVPGEYEGDTYYPEWDAAEWELDAETDHEGFTLQEWVRS---- 157 HHsearch alignment (Probability: 0.04 E-value:0.04) d1t6t1_ 17 EAVILVEGKNDKKALSKFSIKNVIDLSGKRYADVVDMLEGKWEKVILL 64 :::::::::::::::::::::::::::::::: :::::::::::::: d1vdra_ 73 DTAHRAASVEEAVDIAASLDAETAYVIGGAAI--YALFQPHLDRMVLS 118