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 <-- 1.307 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1rq2a1) 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 d1rq2a1 Cell-​division protein FtsZTubulin nucleotide-​binding domain-​likeTubulin nucleotide-​binding domain-​likeα/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 <-- 1.307 --> Hit
DALI alignment (Z-score: 7.6 Raw score:651.70) d1im5a_ 1 PEEALIVVDMqrdfmpggalpvpegdkiipKVNEYIRKfkEKGALIVATRDWhpenhisf 60 :::::::::: :::::::: :::::::::::: d1rq2a1 1 AVIKVVGIGG----------------ggvnAVNRMIEQ-gLKGVEFIAINTD-------- 35 d1im5a_ 61 rerggpwprhcvqntpGAEF-VVDLpedAVIISKATEP-------dkEAYSgfEGTDLAK 112 :::: :::: :::::::::: :::: ::::::: d1rq2a1 36 ----------------AQALlMSDA---DVKLDVGRDStgadpevgrKAAE-dAKDEIEE 75 d1im5a_ 113 ILRgnGVKRVYICGV----atEYCVRATALDALKHGFEVYLLrdaVKGI-------KPED 161 ::: :::::::::: ::::::::::::::::::::: :::: :::: d1rq2a1 76 LLR--GADMVFVTAGegggtgTGGAPVVASIARKLGALTVGV---VTRPfsfegkrRSNQ 130 d1im5a_ 162 EERALEEMKSrgIKIV-------------------------------------------- 177 :::::::::: :::: d1rq2a1 131 AENGIAALREscDTLIvipndrllqmgdaavslmdafrsadevllngvqgitdlittpgl 190 d1im5a_ 178 qf 179 d1rq2a1 191 in 192 FAST alignment (Normalized score: 6.18 Raw score:1146.00) d1im5a_ 1 PEEALIVVDMQRDFMPGGALPVPEGDKII-PKVNEYIRKFKEK---GALIVATRDWHPEN 56 :::::::: ::::::::::::: :::::::: d1rq2a1 1 AVIKVVGI---------------------GGGGVNAVNRMIEQGLKGVEFIAIN------ 33 d1im5a_ 57 HISFRERGGPWPRHCVQNTPGAE------FVVDLPED-AVIISKATEPDKEAYSGFEG-- 107 :::: ::::::: d1rq2a1 34 -----------------------TDAQALLMSD----ADVKLDVG-------------RD 53 d1im5a_ 108 -----------------TDLAKILRGNGVKRVYICGV-----ATEYCVRATALDALKHGF 145 ::::::: :::::::::: :::::::::::::::::: d1rq2a1 54 STGADPEVGRKAAEDAKDEIEELL--RGADMVFVTA-GEGGGTGTGGAPVVASIARKLGA 110 d1im5a_ 146 EVYLLRDAVKGI------------KPEDEERALEEMKSRG--IKIVQF------------ 179 :::: :::::::::::::: :::: d1rq2a1 111 LTVG--------VVTRPFSFEGKRRSNQAENGIAALRE--SCDTLI--VIPNDRLLQMGD 158 d1im5a_ 180 ---------------------------------- 180 d1rq2a1 159 AAVSLMDAFRSADEVLLNGVQGITDLITTPGLIN 192 TMalign alignment (TM-score: 0.55 Raw score:98.22) d1im5a_ 1 PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATRDWHPENHISF 60 :::::::::: :: :: :::::::: :::::::::::: d1rq2a1 1 AVIKVVGIGG--------------GG-VN-AVNRMIEQ-GLKGVEFIAINT--------- 34 d1im5a_ 61 RERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPD-----KE--AYSGFEGTDLAKI 113 : :::::::: :::::::::::: : ::::::::::::: d1rq2a1 35 ----------D------AQALLMSD-ADVKLDVGRDSTGADPE-VGRKAAEDAKDEIEEL 76 d1im5a_ 114 LRGNGVKRVYICGV--A--TEYCVRATALDALKHGFEVYLLRDAVK---G--IKPEDEER 164 :: :::::::::: : :::::::::::::::::::::::: :: : :::::::: d1rq2a1 77 LR--GADMVFVTAGEGGGTGTGGAPVVASIARKLGALTVGVVT-RPFSFEGKRRSNQAEN 133 d1im5a_ 165 ALEEMKSRGIKIV------------------------------Q--F------------ 179 ::::::::::::: : : d1rq2a1 134 GIAALRESCDTLIVIPNDRLLQMGDAAVSLMDAFRSADEVLLNGVQGITDLITTPGLIN 192 HHsearch alignment (Probability: 0.01 E-value:0.56) d1im5a_ 39 FKEKGALIV 47 ::::::::: d1rq2a1 105 ARKLGALTV 113