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 <-- 0.752 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1j2ra_) 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 d1j2ra_ Hypothetical protein YecDIsochorismatase-​like hydrolasesIsochorismatase-​like hydrolasesα/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 <-- 0.752 --> Hit
DALI alignment (Z-score: 22.1 Raw score:1627.60) d1im5a_ 1 ------PEEALIVVDMQRDFMpggaLPVP---EGDKIIPKVNEYIRKFKEKGALIVATRD 51 ::::::::::::::: :::: :::::::::::::::::::::::::::: d1j2ra_ 1 mlelnaKTTALVVIDLQEGIL----PFAGgphTADEVVNRAGKLAAKFRASGQPVFLVRV 56 d1im5a_ 52 WHPENHIsfrERGG--PWPRhcvQNTPGAEFV--VDLPEDAVIISKAtepdkeAYSGFEG 107 ::::::: :::: :::: ::::::::: ::::::::::::: ::::::: d1j2ra_ 57 GWSADYAealKQPVdaPSPA-kvLPENWWQHPaaLGTTDSDIEIIKR------QWGAFYG 109 d1im5a_ 108 TDLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERAL- 166 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1j2ra_ 110 TDLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFNLVIAEDACSAASAEQHNNSIn 169 d1im5a_ 167 EEMKsRGIKIVQF------- 179 :::: :::::::: d1j2ra_ 170 HIYP-RIARVRSVeeilnal 188 FAST alignment (Normalized score: 17.76 Raw score:3258.00) d1im5a_ 1 P-------EEALIVVDMQRDFMPGGALPV-------PEGDKIIPKVNEYIRKFKEKGALI 46 ::::::::::::: :::::::::::::::::::::::: d1j2ra_ 1 -MLELNAKTTALVVIDLQEGI--------LPFAGGPHTADEVVNRAGKLAAKFRASGQPV 51 d1im5a_ 47 VATRDWHPENHISFRERGGPWPRHCV----------------QNTPGAEF--VVDLPEDA 88 ::::::::::: :::::::: :::::::: d1j2ra_ 52 FLVRVGWSADY---------------AEALKQPVDAPSPAKVLPENWWQHPAALGTTDSD 96 d1im5a_ 89 VIISKATEPDKE--AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFE 146 :::: :::::::::::::::::::::::::::::::::::::::::::::: d1j2ra_ 97 IEII--------KRQWGAFYGTDLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFN 148 d1im5a_ 147 VYLLRDAVKGIKPEDEERALE-EMKSRGIKIVQF--------- 179 ::::::::::::::::::::: :::: ::::: d1j2ra_ 149 LVIAEDACSAASAEQHNNSINHIYPR-IARVR--SVEEILNAL 188 TMalign alignment (TM-score: 0.83 Raw score:147.95) d1im5a_ 1 ------PEEALIVVDMQRDFMPGGALPVP---EGDKIIPKVNEYIRKFKEKGALIVATRD 51 :::::::::::::::: ::: :::::::::::::::::::::::::::: d1j2ra_ 1 MLELNAKTTALVVIDLQEGILP----FAGGPHTADEVVNRAGKLAAKFRASGQPVFLVRV 56 d1im5a_ 52 WHPENH--ISF--RERGGPWPRHCVQNTPGAEFV--VDLPEDAVIISKATEPDKEAYSGF 105 :::::: ::: :::::::::: :::::::: ::::::::::::: ::::: d1j2ra_ 57 GWSADYAEALKQP--VDAPSPAKVL-PENWWQHPAALGTTDSDIEIIKR------QWGAF 107 d1im5a_ 106 EGTDLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERA 165 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1j2ra_ 108 YGTDLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFNLVIAEDACSAASAEQHNNS 167 d1im5a_ 166 LE-EMKSRGIKIVQ-F------ 179 :: :::: :::::: : d1j2ra_ 168 INHIYPR-IARVRSVEEILNAL 188 HHsearch alignment (Probability: 1.00 E-value:0.00) d1im5a_ 1 PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATRDWHPENHISF 60 :::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::: d1j2ra_ 7 KTTALVVIDLQEGILPFA-GGPHTADEVVNRAGKLAAKFRASGQPVFLVRVGWSADYAEA 65 d1im5a_ 61 RER-GGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSGFEGTDLAKILRGNGV 119 ::: :::::::::::::::::::::: :::::::::::::::::::::::::::::: d1j2ra_ 66 LKQPVDAPSPAKVLPENWWQHPAALG----TTDSDIEIIKRQWGAFYGTDLELQLRRRGI 121 d1im5a_ 120 KRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERALEEMKSRGIKIVQF 179 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1j2ra_ 122 DTIVLCGISTNIGVESTARNAWELGFNLVIAEDACSAASAEQHNNSINHIYPRIARVRSV 181