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 <-- 0.845 --> Intermediate <-- 1.023 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d2piaa2) through the intermediate protein (d1im5a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1im5a_ Pyrazinamidase/​nicotinamidaseIsochorismatase-​like hydrolasesIsochorismatase-​like hydrolasesα/β
Hit d2piaa2 Phthalate dioxygenase reductaseFerredoxin reductase-​like,​ C-​terminal NADP-​linked domainFerredoxin reductase-​like,​ C-​terminal NADP-​linked domainα/β

Supporting Alignments

Query <-- 0.845 --> Intermediate
DALI alignment (Z-score: 2.3 Raw score:295.90) query 1 ------------------------------------------------------------ 1 d1im5a_ 1 peealivvdmqrdfmpggalpvpegdkiipkvneyirkfkekgalivatrdwhpenhisf 60 query 1 -------------------------------------DADE-evYSALvvGLRAYVAKNG 22 :::: :::: :::::::::: d1im5a_ 61 rerggpwprhcvqntpgaefvvdlpedaviiskatepDKEAysgFEGT--DLAKILRGNG 118 query 23 FRSVLIG-lsGGIDSALVAAIACDALGaqNVYGVSMpskySSDHSKGDAAELARRTGLNF 81 ::::::: ::::::::::::::::: ::::::: :::::::::::::::::::: d1im5a_ 119 VKRVYICgvaTEYCVRATALDALKHGF--EVYLLRDavkgIKPEDEERALEEMKSRGIKI 176 query 82 RTVsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgys 141 ::: d1im5a_ 177 VQF--------------------------------------------------------- 179 query 142 tlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailel 201 d1im5a_ 180 ------------------------------------------------------------ 180 query 202 yvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnr 261 d1im5a_ 180 ------------------------------------------------------------ 180 query 262 wregh 266 d1im5a_ 180 ----- 180 FAST alignment (Normalized score: 2.15 Raw score:469.10) query 1 DADEEVYSALV------------------------------------------------- 11 d1im5a_ 1 -----------PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVAT 49 query 12 ----------------------------------------------------------VG 13 :: d1im5a_ 50 RDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSGFEGTD 109 query 14 LRAYVAKNGFRSVLIGLS----GGIDSALVAAIACDALGAQ---NVYGVSMPSKY----- 61 ::::::::::::::: :::::::::::::: ::::: d1im5a_ 110 LAKILRGNGVKRVYI---CGVATEYCVRATALDALK-----HGFEVYLL------RDAVK 155 query 62 -SSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAIS 120 ::::::::::::::::::::: d1im5a_ 156 GIKPEDEERALEEMKSRGIKIV-------------------------------------- 177 query 121 NQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTP 180 d1im5a_ 178 ------------------------------------------------------------ 178 query 181 PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYP 240 d1im5a_ 178 ------------------------------------------------------------ 178 query 241 PGTKISAKGFGKDRRLPITNRWREGH-- 266 d1im5a_ 178 --------------------------QF 179 TMalign alignment (TM-score: 0.30 Raw score:81.01) query 1 --------------DADE------EVYSALVVGLRAYVAKN-G-FRSVLIGLSGG----- 33 ::: ::: ::::::::::::: : ::::::::::: d1im5a_ 1 PEEALIVVDMQRDF-MPGGALPVPEGD-KIIPKVNEYIRKFKEKGALIVATRDWHPENHI 58 query 34 -----------ID-SA---LVAAIACDALGAQNVYGVSMPSKYSSDHSK---GDAAELAR 75 :: : :::::: ::: :::::::: :::::: d1im5a_ 59 SFRERGGPWPRHCV-QNTPGAEFVV--DLP-EDAVIISK----ATEPDKEAY-------- 102 query 76 RTGLNFRTVSIEPMFDAYMASLGLTGLAEEN-LQSRLRGTTLMAISNQ--EGHIVLAPGN 132 : ::::::::::::::: ::::::: d1im5a_ 103 ------------------------------SG-FEGTDLAKILRGNGVKR---VYICGVA 128 query 133 KSELAVGYSTLYGDS---V-GAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASIT 188 :::: ::::::::: : ::::::::::: d1im5a_ 129 TEYC--VRATALDALKHGFEVYLLRDAVKGI----------------------------- 157 query 189 KPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 248 :: :: :: : :::::::: ::::::: d1im5a_ 158 -------KP-ED-EE----------------------R-ALEEMKSR-GIKIVQF----- 179 query 249 GFGKDRRLPITNRWREGH 266 d1im5a_ 180 ------------------ 180 HHsearch alignment (Probability: 0.10 E-value:0.05) query 13 GLRAYVAKNGFRSVLIGL---SGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGD 69 :::::::::::::::::: ::::::::::::: :::: :::::::::::::::::: d1im5a_ 109 DLAKILRGNGVKRVYICGVATEYCVRATALDALK---HGFE-VYLLRDAVKGIKPEDEER 164 query 70 AAELARRTGLN 80 ::::::::::: d1im5a_ 165 ALEEMKSRGIK 175
Intermediate <-- 1.023 --> Hit
DALI alignment (Z-score: 4.5 Raw score:367.90) d1im5a_ 1 --------pEEALIVVDMqrdfmpggalpvpegdkiipKVNEYIRKFKE---KGALIVAT 49 ::::::::: ::::::::::: :::::::: d2piaa2 1 efpldkrakSFILVAGGI-----------------gitPMLSMARQLRAeglRSFRLYYL 43 d1im5a_ 50 RDWhpenhisfrerggpwprhcvqntpGAEFV------vdlPEDAVIISKATEpdkeays 103 ::: ::::: :::::::::::: d2piaa2 44 TRD-----------------------pEGTAFfdeltsdewRSDVKIHHDHGD------- 73 d1im5a_ 104 gfeGTDLAKILRGNG-vKRVYICGvateycVRATALDALKHG-----fEVYLLrdavkgi 157 :::::::::::: ::::::: :::::::::::: ::::: d2piaa2 74 ptkAFDFWSVFEKSKpaQHVYCCG------PQALMDTVRDMTghwpsgTVHFE------- 120 d1im5a_ 158 kpedeeraleemksrgikivqf 179 d2piaa2 121 ---------------------- 121 FAST alignment (Normalized score: 4.14 Raw score:606.90) d1im5a_ 1 --------PEEALIVVDMQRDFMPGGALPVPEGDK--IIPKVNEYIRKFKE---KGALIV 47 :::::::: :::::::::::::: :::::: d2piaa2 1 EFPLDKRAKSFILVAG-------------------GIGITPMLSMARQLRAEGLRSFRLY 41 d1im5a_ 48 ATRDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLP------------------EDAV 89 ::: :::: d2piaa2 42 YLT-----------------------------------RDPEGTAFFDELTSDEWRSDVK 66 d1im5a_ 90 IISKATEPDKEAYSGFE-------GTDLAKILRGNGV----KRVYICGVATEYCVRATAL 138 ::: :::::::::: ::::::: :::::: d2piaa2 67 IHH--------------DHGDPTKAFDFWSVFEK---SKPAQHVYCCG------PQALMD 103 d1im5a_ 139 DALKHGF--------EVYLLRDAVKGIKPEDEERALEEMKSRGIKIVQF- 179 :::: :::: d2piaa2 104 TVRD---MTGHWPSGTVHF------------------------------E 120 TMalign alignment (TM-score: 0.41 Raw score:74.05) d1im5a_ 1 --------PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFK--E-KGALIVAT 49 :::::::::: : :: :::::::::: : :::::::: d2piaa2 1 EFPLDKRAKSFILVAGGI--------------G--IT-PMLSMARQLRAEGLRSFRLYYL 43 d1im5a_ 50 RDWHPENHISFRERGGPWPRHCVQNTPGAEFVV-DL----PED-AVIISKATEPDKEAYS 103 ::: : : ::::: :: ::: :::::: :: ::: d2piaa2 44 TRD---------------------P-E-GTAFFDELTSDEWRSDVKIHHD-HG--DPT-- 75 d1im5a_ 104 GFEGTDLAKILRGNGV--KRVYICGVATEYCVRATALDALKHG--F---EVYLLRDAVKG 156 ::::::: :::::: ::::::: : ::::::::::: : ::::: d2piaa2 76 --KAFDFWS-VFEKSKPAQHVYCCG-----P-QALMDTVRDMTGHWPSGTVHFE------ 120 d1im5a_ 157 IKPEDEERALEEMKSRGIKIVQF 179 d2piaa2 121 ----------------------- 121 HHsearch alignment (Probability: 0.04 E-value:0.10) d1im5a_ 29 IPKVNEYIRKFKEKGA 44 :::::::::::::::: d2piaa2 20 ITPMLSMARQLRAEGL 35