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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.022 --> Intermediate <-- 1.755 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1a04a2) through the intermediate protein (d1ujpa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ujpa_ Trp synthase alpha-​subunitRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1a04a2 Nitrate/​nitrite response regulator (NarL),​ receiver domainCheY-​likeFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 1.022 --> Intermediate
DALI alignment (Z-score: 9.2 Raw score:936.30) query 1 mietpyylidkakltrnmeriahvrEKSGAKALLALK-----cfaTWSVFDLMRDYMDGT 55 :::::::::::: ::::::::::::::: d1ujpa_ 1 --------------mttleafakarSEGRAALIPYLTagfpsregFLQAVEEVLPYADLL 46 query 56 TSSS-------------------------LFEVRLGRERFGKETHAYSVA------yGDN 84 :::: ::::::::::::::::::::: ::: d1ujpa_ 47 EIGLpysdgpviqraselalrkgmsvqgaLELVREVRALTEKPLFLMTYLnpvlawgPER 106 query 85 EIDEVVS-HADKIIF-NSIS-qlERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDR 139 ::::::: ::::::: :::: :::::::: ::::::::::: :::::::::::: d1ujpa_ 107 FFGLFKQaGATGVILpDLPPdedPGLVRLAQeiGLETVFLLAPT----STDARIATVVRH 162 query 140 IN-GFMIHNNcenkdfglfdrMLGEIEERFGALIArvDWVSLGGGIHFtgddypvDAFSA 198 :: ::::::: :::::::::::::: ::::::::::: ::::: d1ujpa_ 163 ATgFVYAVSV-----------EVKDLVRRIKARTA--LPVAVGFGVSG-------KATAA 202 query 199 RLRafsdrygvqIYLEPGEASI-TKSTtlevtvldtlynknlaivdssieahmldlliyr 257 ::: :::::::::: :::: d1ujpa_ 203 QAA-------vaDGVVVGSALVrALEE--------------------------------- 222 query 258 etakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGytmvkknwfng 317 :::: d1ujpa_ 223 ---------------------------------------------GRSL----------- 226 query 318 vkmpaiaireldgsvrtvreftyadyeqsls 348 d1ujpa_ 227 --------------apllqeirqglqrlplp 243 FAST alignment (Normalized score: 5.49 Raw score:1595.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS--------------GAKALLALKCFA------ 40 ::::::: d1ujpa_ 1 ----------------------------MTTLEAFAKARSEGRAALIPY-----LTAGFP 27 query 41 ----TWSVFDLMRDYMDGTTSS--------------------------SLFEVRLGRERF 70 ::::::::::::::::: :::::::::::: d1ujpa_ 28 SREGFLQAVEEVLPYADLLEI-GLPYSDGPVIQRASELALRKGMSVQGALELVREVRALT 86 query 71 GKETHAYSVAY---------GDNEIDEVVS-HADKIIFNSIS--QLERFADKA-----AG 113 :::::::: :::::::::: :::::::: ::::::::: :: d1ujpa_ 87 EKPLFLMT---YLNPVLAWGPERFFGLFKQAGATGVILP---DLPPDEDPGLVRLAQEIG 140 query 114 IARGLRLNPQRLGE-WDVPKVERVMDR-INGFMIHNNCENKDFG--LFDRMLGEIEERFG 169 ::::::::: :::::::::::: ::::::: :::::::::::: d1ujpa_ 141 LETVFLLAP-----TSTDARIATVVRHATGFVYAV---------SVEVKDLVRRIKAR-- 184 query 170 ALIARV--DWVSLGGGIHFTGDDYP-----VDAFSARLRAFSDRYGVQ-IYLEPGEASIT 221 ::::: :::::::::: ::::::::: d1ujpa_ 185 ------TALPVAV------------GFGVSGKATAAQAAV--------ADGVVVGSAL-- 216 query 222 KSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAG 281 d1ujpa_ 217 ------------------------------------------------------------ 217 query 282 DVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYA 341 d1ujpa_ 217 ------------------------------------------------------------ 217 query 342 DYEQSLS--------------------------- 348 d1ujpa_ 217 -------VRALEEGRSLAPLLQEIRQGLQRLPLP 243 TMalign alignment (TM-score: 0.36 Raw score:126.07) query 1 ------------------------------------------------------------ 1 d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQR 60 query 1 ----------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-FAT---WSV-F 45 :::::::::::::::::::::::::: ::: ::: : d1ujpa_ 61 ASELALRKGM------------SVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFF 108 query 46 DLMRDY-MDGTTSS-SLF-EVRLGRERFG---KETHAYSVA-YGDNEIDEVVSHA-DKII 97 :::::: ::::::: ::: :::::::::: ::::::::: ::::::::::::: :::: d1ujpa_ 109 GLFKQAGATGVILPDLPPDEDPGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVY 168 query 98 FN---SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHN-NCENKD 153 :: :::::::::::: ::::::::::: ::::::::: : :::::::: :::: : d1ujpa_ 169 AVSVEVKDLVRRIKART-ALPVAVGFGVS--GKATAAQAA--V--ADGVVVGSALVRA-L 220 query 154 FGLFDRMLGEIEERFGALIAR----VDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGV 209 ::: ::::::::: ::::::: d1ujpa_ 221 EEG-RSLAPLLQE-IRQGLQRLPLP----------------------------------- 243 query 210 QIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSH 269 d1ujpa_ 244 ------------------------------------------------------------ 244 query 270 SYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELD 329 d1ujpa_ 244 ------------------------------------------------------------ 244 query 330 GSVRTVREFTYADYEQSLS 348 d1ujpa_ 244 ------------------- 244 HHsearch alignment (Probability: 0.04 E-value:0.64) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFE----VRLGRERFGKET 74 :::::::::::::::::::::::::::::::::::::::::::: :::::::::::: d1ujpa_ 130 PGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPV 189 query 75 HAYSVAYGDNEIDEVVSHADKII 97 ::::::::::::::::::::::: d1ujpa_ 190 AVGFGVSGKATAAQAAVADGVVV 212
Intermediate <-- 1.755 --> Hit
DALI alignment (Z-score: 5.0 Raw score:465.60) d1ujpa_ 1 mttleafakarsegRAALIPYLT----------------------agFPSREGFLQAVEE 38 ::::::::: ::::::::::::: d1a04a2 1 --------------EPATILLIDdhpmlrtgvkqlismapditvvgeASNGEQGIELAES 46 d1ujpa_ 39 VLpyADLLEIGLPysdgpviqraselalrkGMSVqgALELVREVRAL-TEKPLFLMTYLN 97 :: ::::::::: :::: ::::::::::: :::::::::::: d1a04a2 47 LD--PDLILLDLN----------------mPGMN--GLETLDKLREKsLSGRIVVFSVSN 86 d1ujpa_ 98 pvlawgPERFFGLFKQAGATGVILPDlppdedpglvrlaqeigletvFLLAptstdaria 157 :::::::::::::::::::: :::: d1a04a2 87 ------HEEDVVTALKRGADGYLLKD---------------------MEPE--------- 110 d1ujpa_ 158 tvvrhatgfVYAVsvevkdlvrrikartalpVAVGfgvsgkataaqaavadgvvvgsalv 217 :::: :::: d1a04a2 111 ---------DLLK------------------ALHQ------------------------- 118 d1ujpa_ 218 raleegrslapllqeirqglqrlplp 243 d1a04a2 119 ------aaagemvlsealtpvlaasl 138 FAST alignment (Normalized score: 4.78 Raw score:875.20) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGF---------------------------PSREGFL 33 ::::::: ::::::: d1a04a2 1 --------------EPATILL-----IDDHPMLRTGVKQLISMAPDITVVGEASNGEQGI 41 d1ujpa_ 34 QAVEEVLP-YADLLEIGLPYSDGPVIQRASELALRKGMSV-----QGALELVREVRA-LT 86 ::::: :::::::: :::::::::::: :: d1a04a2 42 ELAES---LDPDLILLD-----------------------LNMPGMNGLETLDKLREKSL 75 d1ujpa_ 87 EKPLFLMTYLNPVLAWG---PERFFGLFKQAGATGVILPDLPPDEDPGL----------- 132 :::::::: ::::::::::::::::::::: d1a04a2 76 SGRIVVFS---------VSNHEEDVVTALKRGADGYLLKDM--------EPEDLLKALHQ 118 d1ujpa_ 133 --------VRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKAR 184 :::::: d1a04a2 119 AAAGEMVLSEALTP---------------------------------------------- 132 d1ujpa_ 185 TALPVAVGFGVSGKATAAQAAVADGVVVGSALVRALEEGRSLAPLLQEIRQGLQRLPLP- 243 d1a04a2 133 -----------------------------------------------------------V 133 d1ujpa_ 244 ----- 244 d1a04a2 134 LAASL 138 TMalign alignment (TM-score: 0.33 Raw score:80.53) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQ- 59 ::: :::::::::::::: d1a04a2 1 ----------------------------------------EPA--TILLIDDHPMLRTGV 18 d1ujpa_ 60 RA-------------SELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVLAWGPER 106 : :: :::::::::::::: : :::::: ::::::::: : d1a04a2 19 -KQLISMAPDITVVG---EA---SNGEQGIELAESLD--P--DLILLD-LNMPGMNGL-E 65 d1ujpa_ 107 FFGLFKQA-G-ATGVILPDLPPDEDPGLVRLAQEIGLETVFL--LAPTSTDARIATVVRH 162 :::::::: : :::::: ::: ::::::::::::::::::: ::: d1a04a2 66 TLDKLREKSLSGRIVVF-SVS--NHEEDVVTALKRGADGYLLKDMEP------------- 109 d1ujpa_ 163 ATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKATAAQAAVADGVV----------- 211 :::: ::: :::: d1a04a2 110 -----EDLL-----------------KAL----------------HQAAAGEMVLSEALT 131 d1ujpa_ 212 -------VGSALVRALEEGRSLAPLLQEIRQGLQRLPLP 243 d1a04a2 132 PVLAASL-------------------------------- 138 HHsearch alignment (Probability: 0.64 E-value:0.00) d1ujpa_ 21 YLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQRASELALRKGMSVQGALELVR 80 ::::::::::::::::::::::::::::::::::: ::::: d1a04a2 29 TVVGEASNGEQGIELAESLDPDLILLDLNMPGMNG--------------------LETLD 68 d1ujpa_ 81 EVRALT-EKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQEI 139 :::::: ::::::::::: :::::::::::::::::::::::::::::::::::: d1a04a2 69 KLREKSLSGRIVVFSVSN------HEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAG 122 d1ujpa_ 140 G 140 : d1a04a2 123 E 123