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 <-- 0.634 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1nrza_) 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 d1nrza_ Sorbose permease subunit IIb ,​ EIIb-​sorPTS IIb componentPTS IIb componentα/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 <-- 0.634 --> Hit
DALI alignment (Z-score: 4.2 Raw score:381.30) d1im5a_ 1 PEEALivvdmqrdfmpggalpvpegdkiIPKVNEYIRKFKekgALIVAT----RDWHpen 56 ::::: :::::::::::: :::::: :::: d1nrza_ 1 MQITL--------------ariddrlihGQVTTVWSKVAN---AQRIIIcnddVFND--- 40 d1im5a_ 57 hisfrerggpwprhcvqnTPGAEF-vvDLPE-DAVIISkatepdkeaysGFEGtdLAKIL 114 :::::: :::: :::::: :::: ::::: d1nrza_ 41 ------------------EVRRTLlrqAAPPgMKVNVV-----------SLEK--AVAVY 69 d1im5a_ 115 RGngvkrvyicgvateyCVRATALDALKHGFEV-YLLRdAVKG------------IKPED 161 :: :::::::::::::::: :::: :::: ::::: d1nrza_ 70 HN---pqyqdetvfylfTNPHDVLTMVRQGVQIaTLNI-GGMAwrpgkkqltkavSLDPQ 125 d1im5a_ 162 EERALEEMKSRGIKIVQF-------------------- 179 :::::::::::::::::: d1nrza_ 126 DIQAFRELDKLGVKLDLRvvasdpsvnildkinetafc 163 FAST alignment (Normalized score: 3.45 Raw score:589.10) d1im5a_ 1 PEE---ALIVVDMQRDFMPGGALPVPEGDKIIPK------VNEYIRKFKEKG----ALIV 47 :::: :::::::::: :::: d1nrza_ 1 ---MQITLAR------------------------IDDRLIHGQVTTVWSK--VANAQRII 31 d1im5a_ 48 ATRDWHPENHISFRERGGPWPRHCVQN------TPGAEFVV-----DLPEDAVIISKATE 96 ::: :::: :::::::::: d1nrza_ 32 ICN------------------------DDVFNDEVRR----TLLRQAAPPGMKVNV---- 59 d1im5a_ 97 PDKEAYSGFEG---TDLAKILRGNGVKRVYICGVATEYC--------------VRATALD 139 :::::::: ::::::: d1nrza_ 60 -----------VSLEKAVAVYH-----------------NPQYQDETVFYLFTNPHDVLT 91 d1im5a_ 140 ALKHGFE-VYLLR--------------DAVKGIKPEDEERALEEMKSRGIKIVQF----- 179 ::::::: :::: ::::: ::::::::::::::::::: d1nrza_ 92 MVRQGVQIATLN-IGGMAWRPGKKQLTKAVSL--DPQDIQAFRELDKLGVKLD--LRVVA 146 d1im5a_ 180 ----------------- 180 d1nrza_ 147 SDPSVNILDKINETAFC 163 TMalign alignment (TM-score: 0.50 Raw score:89.50) d1im5a_ 1 PEEALIVVDMQRDFMPGGALPVPEGDKII-PKVNEYIRKFKEKGALIVATRDWHPENHIS 59 :::::::: : ::::: ::::::::::: :::::::::: d1nrza_ 1 MQITLARI-D--------------DRLIHGQVTTVWSKVAN---AQRIIICNDD------ 36 d1im5a_ 60 FRERGGPWPRHCVQNTPGAE-FVVDLP-EDAVIISKATEPDKEAYSGFEGTDLAKILRGN 117 :::: ::::: :::::: ::::::::: : ::: :::::::::: d1nrza_ 37 ----------VFND-EVRRTLLRQAAPPGMKVNVVSL------E-KAV--AVYHNPQYQD 76 d1im5a_ 118 GVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKG-I--K--------P-EDEERA 165 :: ::::::::: :::::::: :: ::::::: :::: : : : :::::: d1nrza_ 77 ET--VFYLFTNPH-DVLTMVRQ--GV-QIATLNI-GGMAWRPGKKQLTKAVSLDPQDIQA 129 d1im5a_ 166 LEEMKSRGIKIV-Q--F----------------- 179 :::::::::::: : : d1nrza_ 130 FRELDKLGVKLDLRVVASDPSVNILDKINETAFC 163 HHsearch alignment (Probability: 0.02 E-value:0.12) d1im5a_ 110 LAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERALEEM 169 :::::::::::::::::::::::: ::::::::: ::: :::::::: d1nrza_ 90 LTMVRQGVQIATLNIGGMAWRPGK--------------KQLTKAVSL-DPQ-DIQAFREL 133 d1im5a_ 170 KSRGIKIV 177 :::::::: d1nrza_ 134 DKLGVKLD 141