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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.211 --> Intermediate <-- 0.918 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1spva_) through the intermediate protein (d1ii7a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ii7a_ Mre11Metallo-​dependent phosphatasesMetallo-​dependent phosphatasesα+β
Hit d1spva_ Hypothetical protein YmbDMacro domain-​likeMacro domain-​likeα/β

Supporting Alignments

Query <-- 1.211 --> Intermediate
DALI alignment (Z-score: 7.2 Raw score:832.10) query 1 slqLRLALNQIDS-TVGD------IAGNAEAILRWTRHSAEQGAHLVAFPEMALTgypve 53 :::::::::: :::: ::::::::::::::::::::::::::::::: d1ii7a_ 1 ---MKFAHLADIHlGYEQfhkpqrEEEFAEAFKNALEIAVQENVDFILIAGDLFH----- 52 query 54 dlalrssFVEASRTALRELAARLAeegFGELPVLV---gyLDRSesaqpkygqpaGAPRN 110 ::::::::::::::::: :::::::: :::: ::::: d1ii7a_ 53 ----ssrPSPGTLKKAIALLQIPK---EHSIPVFAiegnhDRTQ-----------RGPSV 94 query 111 AaavlhrgRVALTfakhhlpnygvfdefryfvpgDTMPIVRLHGVDIALAICE----dlw 166 : ::::: ::::::::::::::::::: d1ii7a_ 95 L-nlledfGLVYVigmrkekveneyltserlgngEYLVKGVYKDLEIHGMKYMssawfea 153 query 167 QDGGRVPAARsagaGLLLSV---naspyERDKDDTrleLVRKRAqEAGCT-TAYLAMIgg 222 :::::::::: :::::: ::::::: :::::: ::::: ::::::: d1ii7a_ 154 NKEILKRLFRptdnAILMLHqgvrevseARGEDYF--eIGLGDL-PEGYLyYALGHIH-- 208 query 223 qdelvfDGDSivvdrDGEVVARA--------------------------pqFSEGCVVLD 256 :::: :::::::: ::::::::: d1ii7a_ 209 ------KRYE---tsYSGSPVVYpgslerwdfgdyevryewdgikfkerygVNKGFYIVE 259 query 257 LdlpaaeaepptgvvddglridrlviseeplpayeaeLAGGyadrldadeevysalvvgl 316 : :::: d1ii7a_ 260 D------------------------------------FKPR------------------- 264 query 317 rayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaela 376 d1ii7a_ 265 ------------------------------------------------------------ 265 query 377 rrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnks 436 d1ii7a_ 265 ------------------------------------------------------------ 265 query 437 elavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypv 496 d1ii7a_ 265 ------------------------------------------------------------ 265 query 497 ldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdr 556 d1ii7a_ 265 ---fveikvrpfidvkikgseeeirkaikrliplipknayvrlnigwrkpfdlteikell 321 query 557 rlpitnrwregh 568 d1ii7a_ 322 nveylkidtwri 333 FAST alignment (Normalized score: 2.90 Raw score:1260.00) query 1 SLQLRLALNQIDSTVG--------------DIAGNAEAILRWTRHSAEQGAHLVAFPEMA 46 :::::: :::::::::::::::::::::::::::::: d1ii7a_ 1 ---MKFAHL-------ADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDL 50 query 47 LTGYPVEDLALRSSF------VEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPK 100 ::::::::::::::::: ::::::: d1ii7a_ 51 ---------------FHSSRPSPGTLKKAIALLQIPKE---HSIPVFA------------ 80 query 101 YGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPG---------------- 144 d1ii7a_ 81 --------------------------------------------IEGNHDRTQRGPSVLN 96 query 145 -------------------------------DTMPIVRLHGVDIALAICEDLW------- 166 ::::::::::::::::: d1ii7a_ 97 LLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMK-----YMSSAWF 151 query 167 --QDGGRVPAARSAGA------GLLLSVNASPYERDKDDT--------------RLELVR 204 :::::::: ::::::::: :::: d1ii7a_ 152 EANKEILKRL------FRPTDNAILMLHQGV---------REVSEARGEDYFEIGLGD-- 194 query 205 KRAQEA----GCTTAYLAMIGGQDELVFD---GDSIVVDRDGEVVARAPQ---------- 247 :::::: :::::: d1ii7a_ 195 ------LPEGYLYYAL-------------GHIHKRYET------------SYSGSPVVYP 223 query 248 ---------------------------FSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRL 280 :::::::: d1ii7a_ 224 GSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIV------------------------- 258 query 281 VISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSAL 340 d1ii7a_ 259 ------------------------------------------------------------ 259 query 341 VAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLG 400 d1ii7a_ 259 ------------------------------------------------------------ 259 query 401 LTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVY 460 d1ii7a_ 259 ------------------------------------------------------------ 259 query 461 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 520 d1ii7a_ 259 ------------------------------------------------------------ 259 query 521 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH------------ 568 d1ii7a_ 259 ------------------------------------------------EDFKPRFVEIKV 270 query 569 ------------------------------------------------------------ 569 d1ii7a_ 271 RPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDT 330 query 569 --- 569 d1ii7a_ 331 WRI 333 TMalign alignment (TM-score: 0.35 Raw score:198.57) query 1 SLQLRLALNQIDSTVGD-------IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVE 53 :::::::::::::: ::::::::::::::::::::::::::::: :: : d1ii7a_ 1 ---MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDL-FH--S- 53 query 54 DLALRSSFVEASRTALRELAARLAEEGFGELPVLVGY---LDRSESAQPKYGQPAGAPRN 110 : : ::::::::::::::::: :: :::::::: ::: : :::: d1ii7a_ 54 --S-R--PSPGTLKKAIALLQIPK--EH-SIPVFAIEGNHDRT---------Q---RGPS 93 query 111 AAAVLHRGRVALTFAKH----------------HLPNYGVFDEFRYFVPGDTMPIVRLHG 154 ::::::::::::::::: ::::::::::: d1ii7a_ 94 VLNLLEDFGLVYVIGMRKEKVENEYLTSERLGN----------------GEYLVKGVYKD 137 query 155 VDIALAICEDL--W--QDGGRVPAARSAGAGLLLSVNASP--YERDKDDT-R-LELVRKR 206 ::::::::::: : ::::::::::: :::::::::::: :::::::: : :::::: d1ii7a_ 138 LEIHGMKYMSSAWFEANKEILKRLFRP-TDNAILMLHQGVREVSEARGEDYFE-IGLGDL 195 query 207 AQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQ------------------- 247 :: :::::::::: :::::::: ::::::::: d1ii7a_ 196 PE--GYLYYALGHI-------HKRYETSY---SGSPVVYPGSLERWDFGDYEVRYEWDGI 243 query 248 -------FSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYA- 299 ::::::::::: ::::: d1ii7a_ 244 KFKERYGVNKGFYIVEDF------------------------------------KPRFVE 267 query 300 --DRLDADEEVYSALVV-GLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYG 356 : ::: : :::: d1ii7a_ 268 IK--------------VR-PFI---------D-----------VKIK------------- 279 query 357 VSMPSKYSSDHSKGDAAELARRTGLN--------------FRTVSIEPMFDAYMASLGLT 402 :::::::::::::::: d1ii7a_ 280 ----------GSEEEIRKAIKRLIPLIPKNAYVRLNIGWR-------------------- 309 query 403 GLAEENLQSRLRGTTLMAISNQ-E-GHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVY 460 :: : :::::::: : :::::::: :: d1ii7a_ 310 -------KP--F--DLTEIKELLNVEYLKIDTW----------RI--------------- 333 query 461 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 520 d1ii7a_ 334 ------------------------------------------------------------ 334 query 521 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1ii7a_ 334 ------------------------------------------------ 334 HHsearch alignment (Probability: 0.04 E-value:0.06) query 19 AGNAEAILRWTRHSAEQGAHLVAF 42 :::::::::::::::::::::::: d1ii7a_ 23 EEFAEAFKNALEIAVQENVDFILI 46
Intermediate <-- 0.918 --> Hit
DALI alignment (Z-score: 2.9 Raw score:359.30) d1ii7a_ 1 -------------mkFAHLAD--------------------------------------- 8 :::::: d1spva_ 1 trihvvqgditklavDVIVNAanpslmggggvdgaihraagpalldaclkvrqqqgdcpt 60 d1ii7a_ 9 -----------------ihlgYEQFHK-PQREEEFAEAFKNALEIAVQENVDFILIAgdL 50 :::::: ::::::::::::::::::::::::::::: : d1spva_ 61 ghavitlagdlpakavvhtvgPVWRGGeQNEDQLLQDAYLNSLRLVAANSYTSVAFP--A 118 d1ii7a_ 51 FHS---srPSPGTLKKAIALLQ-IPKEHS--IPVFAIEGNhdrtqrgpSVLNLLEDFGlv 104 ::: :::::::::::::: :::::: ::::::::: :::::::::: d1spva_ 119 ISTgvygyPRAAAAEIAVKTVSeFITRHAlpEQVYFVCYD----eenaHLYERLLTQQ-- 172 d1ii7a_ 105 yvigmrkekveneyltserlgngeylvkgvykdleihgmkymssawfeankeilkrlfrp 164 d1spva_ 173 ------------------------------------------------------------ 173 d1ii7a_ 165 tdnailmlhqgvrevseargedyfeiglgdlpegylyyalghihkryetsysgspvvypg 224 d1spva_ 173 ------------------------------------------------------------ 173 d1ii7a_ 225 slerwdfgdyevryewdgikfkerygvnkgfyivedfkprfveikvrpfidvkikgseee 284 d1spva_ 173 ------------------------------------------------------------ 173 d1ii7a_ 285 irkaikrliplipknayvrlnigwrkpfdlteikellnveylkidtwri 333 d1spva_ 173 ------------------------------------------------- 173 FAST alignment (Normalized score: 2.48 Raw score:594.40) d1ii7a_ 1 MK---------------FAHL--------------------------------------- 6 :::: d1spva_ 1 --TRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDC 58 d1ii7a_ 7 ------------------ADIHLGYEQFHK--------PQREEEFAEAFKNALEIAVQEN 40 :::: :::::::::::::::::::::: d1spva_ 59 PTGHAVITLAGDLPAKAVVHTV--------GPVWRGGEQNEDQLLQDAYLNSLRLVAANS 110 d1ii7a_ 41 VDFILIAGDLFHSSRP----------SPGTLKKAIAL-LQIPKEHS--IPVFAIEGNHDR 87 ::::::: ::::::::::: :::::::: :::::: d1spva_ 111 YTSVAFP---------AISTGVYGYPRAAAAEIAVKTVSEFITRHALPEQVYFV------ 155 d1ii7a_ 88 TQRGP----SVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGM 143 :::::::: d1spva_ 156 -----CYDEENAHLYER------------------------------------------- 167 d1ii7a_ 144 KYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYA 203 d1spva_ 168 ------------------------------------------------------------ 168 d1ii7a_ 204 LGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKP 263 d1spva_ 168 ------------------------------------------------------------ 168 d1ii7a_ 264 RFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNV 323 d1spva_ 168 ------------------------------------------------------------ 168 d1ii7a_ 324 EYLKIDTWRI----- 333 d1spva_ 168 ----------LLTQQ 172 TMalign alignment (TM-score: 0.23 Raw score:77.17) d1ii7a_ 1 -------------MKFAHLAD--------------------------------------- 8 :::::::: d1spva_ 1 TRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDCPT 60 d1ii7a_ 9 ------------------IHLGYEQFH-KPQREEEFAEAFKNALEIAVQENVDFILIAGD 49 ::: ::::: ::::::::::::::::::::::::::::: :: d1spva_ 61 GHAVITLAGDLPAKAVVHTVG-PVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAF-PA 118 d1ii7a_ 50 LFH----SSRPSPGTLKKAIALLQ-IPKE-HS-IPVFAIEGNHDRTQRGPSVLNLLEDFG 102 ::: ::::: ::: ::::::: :::: :: ::::::::: ::: ::::::::::: d1spva_ 119 ISTGVYGYPRAA-AAE-IAVKTVSEFITRHALPEQVYFVCYD--EEN--AHLYERLLTQQ 172 d1ii7a_ 103 LVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLF 162 d1spva_ 173 ------------------------------------------------------------ 173 d1ii7a_ 163 RPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIHKRYETSYSGSPVVY 222 d1spva_ 173 ------------------------------------------------------------ 173 d1ii7a_ 223 PGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSE 282 d1spva_ 173 ------------------------------------------------------------ 173 d1ii7a_ 283 EEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRI 333 d1spva_ 173 --------------------------------------------------- 173 HHsearch alignment (Probability: 0.18 E-value:0.06) d1ii7a_ 78 VFAIEGNHD 86 ::::::::: d1spva_ 17 VIVNAANPS 25