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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.132 --> Intermediate <-- 0.852 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1m1nb_) through the intermediate protein (d1ebda2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ebda2 Dihydrolipoamide dehydrogenaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β
Hit d1m1nb_ Nitrogenase iron-​molybdenum protein,​ beta chain​(​Helical backbone​(​ metal receptorChelatase-​likeα/β

Supporting Alignments

Query <-- 1.132 --> Intermediate
DALI alignment (Z-score: 4.5 Raw score:359.30) query 1 ------------------GMENKKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCAf 42 ::::::::::: ::::::::::::::::::::::: d1ebda2 1 pnfkfsnrildstgalnlGEVPKSLVVIG------gGYIGIELGTAYANFGTKVTILEG- 53 query 43 wgLLLLrdpekasqedkslyeqafssltpreAEELplskmnlggigkkmllemmkeekap 102 :::: :::: d1ebda2 54 --AGEI-----------------------lsGFEK------------------------q 64 query 103 KLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqIMDVK----------------e 146 ::::::::::::::::::: ::::: d1ebda2 65 MAAIIKKRLKKKGVEVVTN-------------------ALAKGaeeredgvtvtyeange 105 query 147 yLKNAleSDLQLFI 160 :::: ::::::: d1ebda2 106 tKTID--ADYVLVT 117 FAST alignment (Normalized score: 4.53 Raw score:620.00) query 1 GMEN----------------------KKMNLLLFSGDYDK---ALASLIIANAAREMEIE 35 ::::: ::::::::::::::::: d1ebda2 1 ----PNFKFSNRILDSTGALNLGEVPKSLVV---------IGGGYIGIELGTAYANFGTK 47 query 36 VTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEM 95 ::::::: d1ebda2 48 VTILEGA----------------------------------------------------- 54 query 96 MKEEKAP----------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVK 145 ::::::::::::::::: ::::: d1ebda2 55 -------GEILSGFEKQMAAIIKKRLKKKGVEVV--------------------TNALA- 86 query 146 EYLKNA----------------------LESDLQLFI-- 160 ::::::: d1ebda2 87 ------KGAEEREDGVTVTYEANGETKTIDADYVL--VT 117 TMalign alignment (TM-score: 0.39 Raw score:62.45) query 1 -------------------GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCA 41 :: :::::::: :::::::::::::::::::::::: d1ebda2 1 PNFKFSNRILDSTGALNLGEV-PKSLVVIG------GGYIGIELGTAYANFGTKVTILEG 53 query 42 FWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEEL-PLSKMNLGGIGKKMLLEMMKEEK 100 : :::: : :::: d1ebda2 54 -A-GEIL----------------------S--GFEKQ----------------------- 64 query 101 APKLSDLLS-GARKKEVKFYAXQL---------------SVEIMGFKKEELFPEVQIM-D 143 :::::: :::::::::::::: :: : d1ebda2 65 ---MAAIIKKRLKKKGVEVVTNALAKGAEEREDGVTVTY-----------------EANG 104 query 144 VKEYLKNALESDLQLFI 160 ::: :: :::::::: d1ebda2 105 ETK--TI--DADYVLVT 117 HHsearch alignment (Probability: 0.18 E-value:0.00) query 22 SLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSK 81 :::::::::::::::::: ::::::: d1ebda2 34 GIELGTAYANFGTKVTIL-----------------------------------EGAGEIL 58 query 82 MNLGGIGKKMLLEMMKEEKA 101 :::::::::::::::::::: d1ebda2 59 SGFEKQMAAIIKKRLKKKGV 78
Intermediate <-- 0.852 --> Hit
DALI alignment (Z-score: 5.2 Raw score:329.00) d1ebda2 1 ------------------------------------------------------------ 1 d1m1nb_ 1 sqqvdkikasyplfldqdykdmlakkrdgfeekypqdkidevfqwtttkeyqelnfqrea 60 d1ebda2 1 ------------------------------------------------------------ 1 d1m1nb_ 61 ltvnpakacqplgavlcalgfektmpyvhgsqgcvayfrsyfnrhfrepvscvsdsmted 120 d1ebda2 1 ------------------------------------------------------------ 1 d1m1nb_ 121 aavfggqqnmkdglqnckatykpdmiavsttcmaevigddlnafinnskkegfipdefpv 180 d1ebda2 1 ------------------------------------------------------------ 1 d1m1nb_ 181 pfahtpsfvgshvtgwdnmfegiaryftlksmddkvvgsnkkinivpgfetylgnfrvik 240 d1ebda2 1 ------------------------------------------------------------ 1 d1m1nb_ 241 rmlsemgvgysllsdpeevldtpadgqfrmyaggttqeemkdapnalntvllqpwhlekt 300 d1ebda2 1 ----------------------------------------pnfkfsnrildstgalnLGE 20 ::: d1m1nb_ 301 kkfvegtwkhevpklnipmgldwtdeflmkvseisgqpipasltkergrlvdmmtdsHTW 360 d1ebda2 21 V-PKSLVVIGGGYIGIELGTAYANFGTKV-TILEGAGEilsgfeKQMAAIIKKRLKKK-- 76 : ::::::::::::::::::::::::::: :::::::: :::::::::::::: d1m1nb_ 361 LhGKRFALWGDPDFVMGLVKFLLELGCEPvHILCHNGN------KRWKKAVDAILAASpy 414 d1ebda2 77 --GVEVVTNALAKgaeeredgvtvtyeangeTKTI---DADYVLV--------------- 116 ::::::::::: :::: ::::::: d1m1nb_ 415 gkNATVYIGKDLW----------------hlRSLVftdKPDFMIGnsygkfiqrdtlhkg 458 d1ebda2 117 ------------------------------------------------------------ 117 d1m1nb_ 459 kefevplirigfpifdrhhlhrsttlgyegamqilttlvnsilerldeetrgmqatdynh 518 d1ebda2 117 ---t 117 d1m1nb_ 519 dlvr 522 FAST alignment (Normalized score: 2.28 Raw score:563.30) d1ebda2 1 PNFKFSNRILDSTGAL-------------------------------------------- 16 d1m1nb_ 1 ----------------SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQ 44 d1ebda2 17 ------------------------------------------------------------ 17 d1m1nb_ 45 WTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNR 104 d1ebda2 17 ------------------------------------------------------------ 17 d1m1nb_ 105 HFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAF 164 d1ebda2 17 ------------------------------------------------------------ 17 d1m1nb_ 165 INNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKIN 224 d1ebda2 17 ------------------------------------------------------------ 17 d1m1nb_ 225 IVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAP 284 d1ebda2 17 ------------------------------------------------------------ 17 d1m1nb_ 285 NALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLT 344 d1ebda2 17 ------------NLGEVP-KSLVVIGG--GYIGIELGTAYANFGTK-VTILEGAGEILSG 60 :::::: :::::: ::::::::::::::::: :::::: d1m1nb_ 345 KERGRLVDMMTDSHTWLHGKRFALW--GDPDFVMGLVKFLLELGCEPVHILCH------- 395 d1ebda2 61 -FEKQMAAIIKKRLKK----KGVEVVTNALAKGAEEREDGVTVTYEANGETK-------- 107 ::::::::::::::: :::::::::: d1m1nb_ 396 NGNKRWKKAVDAILAASPYGKNATVYIGKD----------------------LWHLRSLV 433 d1ebda2 108 -TIDADYVLVT------------------------------------------------- 117 ::::::: d1m1nb_ 434 FTDKPDFM---IGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAM 490 d1ebda2 118 -------------------------------- 118 d1m1nb_ 491 QILTTLVNSILERLDEETRGMQATDYNHDLVR 522 TMalign alignment (TM-score: 0.51 Raw score:59.70) d1ebda2 1 ------------------------------------------------------------ 1 d1m1nb_ 1 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREA 60 d1ebda2 1 ---P-------------------------------------------------------- 1 : d1m1nb_ 61 LTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTED 120 d1ebda2 2 ------------------------------------------------------------ 2 d1m1nb_ 121 AAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPV 180 d1ebda2 2 ---------------------------------------------------NFKFSNRIL 10 d1m1nb_ 181 PFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFET--------- 231 d1ebda2 11 DS---------------------------------------------------------- 12 : d1m1nb_ 232 -YLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTV 290 d1ebda2 13 -----------------------------TGAL--------------------------- 16 : d1m1nb_ 291 LLQPWHLEKTKKFVEGTWKHEVPKLNIPM---GLDWTDEFLMKVSEISGQPIPASLTKER 347 d1ebda2 17 ---------NLG--EV-PKSLVVIGGGYIGIELGTAYANFGTKV-TILEGAGEILSGFEK 63 : :: ::::::::::::::::::::::::::: ::::::::: : d1m1nb_ 348 GRLVDMMTD--SHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNK-----R 400 d1ebda2 64 QMAAIIKKRLKK-K--G--VEVVTNALAKGAEEREDGVTVTYE-ANGETKTIDADYVLV- 116 :::::::::: : : ::::::::::: :::: :::::::::: d1m1nb_ 401 --WKKAVDAILAASPYGKNATVYIGKDLWH---------LRSLV-----FTDKPDFMIGN 444 d1ebda2 117 ------------------------T----------------------------------- 117 : d1m1nb_ 445 SYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERL 504 d1ebda2 118 ------------------ 118 d1m1nb_ 505 DEETRGMQATDYNHDLVR 522 HHsearch alignment (Probability: 0.62 E-value:0.00) d1ebda2 20 EVPKSLVVIGGGYIGIELGTAYANFGTKVTILEGAGE----------ILSGF-------- 61 ::::::::::::::::::::::::::::::::::::: ::::: d1m1nb_ 361 LHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATV 420 d1ebda2 62 --EKQMAAIIKKRLKKKGVEVVTNAL 85 :::: ::::::::::::::::::: d1m1nb_ 421 YIGKDL-WHLRSLVFTDKPDFMIGNS 445