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: T0582_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1o4ta_ | Hypothetical protein TM1287 | RmlC-like cupins | Double-stranded beta-helix | All β |
| Hit | d1nx4a_ | Carbapenem synthase, CarC | Clavaminate synthase-like | Double-stranded beta-helix | All β |
Query <-- 1.463 --> IntermediateDALI alignment (Z-score: 11.6 Raw score:634.20) query 1 meinadftkpVVIDTDQLEWRPSPM-----KGVERRMLDRI--GGEVARATSIVRYAPGS 53 ::::::::::::::: ::::::::::: ::::::::::::::::: d1o4ta_ 1 ----------MVVRSSEITPERISNmrggkGEVEMAHLLSKeaMHNKARLFARMKLPPGS 50 query 54 RFSAHTHD-GGEEFIVLDGVFQDE----HGDYPAGTYVRNPPTTSHVPGSAE--GCTIFV 106 :::::::: ::::::::::::::: :::::::::::::::::::::::: :::::: d1o4ta_ 51 SVGLHKHEgEFEIYYILLGEGVFHdngkDVPIKAGDVCFTDSGESHSIENTGntDLEFLA 110 query 107 KLWQFdpadrtqfsknm 123 ::::: d1o4ta_ 111 VIILL------------ 115 FAST alignment (Normalized score: 8.79 Raw score:1045.00) query 1 MEINADFTKPVVIDTDQLEWRPSPM-------KGVERRMLDRIGGEV--------ARATS 45 ::::::::::::: ::::::::: ::::: d1o4ta_ 1 ----------MVVRSSEITPERI--SNMRGGKGEVEMAHLL------SKEAMHNKARLFA 42 query 46 IVRYAPGSRFSAHTHD-GGEEFIVLDGVFQDE-----HGDYPAGTYVRNPPTTSHVPGS- 98 :::::::::::::::: :::::::::::::: :::::::::::::::::::::: d1o4ta_ 43 RMKLPPGSSVGLHKHEGEFEIYYILLGEGVF-HDNGKDVPIKAGDVCFTDSGESHSIENT 101 query 99 -AEGCTIFVKLWQFDPADRTQFSKNM---- 123 ::::::::: d1o4ta_ 102 GNTDLEFLAV----------------IILL 115 TMalign alignment (TM-score: 0.68 Raw score:84.23) query 1 MEINADFTKPVVIDTDQLEWRPSP-M----KGVERRMLDRIG-----GEVARATSIVRYA 50 :::::::::::::: : :::::::::::: :::::::::: d1o4ta_ 1 ----------MVVRSSEITPERISNMRGGKGEVEMAHLLSKEAMHNK---ARLFARMKLP 47 query 51 PGSRFSAHTHD-GGEEFIVLDGVFQ-D---EHGDYPAGTYVRNPPTTSHVPGSAE--GCT 103 ::::::::::: ::::::::::::: : ::::::::::::::::::::::::: ::: d1o4ta_ 48 PGSSVGLHKHEGEFEIYYILLGEGVFHDNGKDVPIKAGDVCFTDSGESHSIENTGNTDLE 107 query 104 IFVKLWQFDPADRTQFSKNM 123 ::::: :: : d1o4ta_ 108 FLAVI-IL-L---------- 115 HHsearch alignment (Probability: 0.96 E-value:0.00) query 13 IDTDQLEWRPSPMKGVERRMLDRIGGEVARATSI--VRYAPGSRFSAHTHDGG-EEFIVL 69 :::::::::::::::::::::::::::::::::: ::::::::::::::::: :::::: d1o4ta_ 8 ITPERISNMRGGKGEVEMAHLLSKEAMHNKARLFARMKLPPGSSVGLHKHEGEFEIYYIL 67 query 70 DGV----FQDEHGDYPAGTYVRNPPTTSHVPG--SAEGCTIFV 106 ::: ::::::::::::::::::::::::: ::::::::: d1o4ta_ 68 LGEGVFHDNGKDVPIKAGDVCFTDSGESHSIENTGNTDLEFLA 110
Intermediate <-- 0.663 --> HitDALI alignment (Z-score: 4.0 Raw score:379.60) d1o4ta_ 1 -------------------------mvvrsseitperisnmrggkgevemahllskeamh 35 d1nx4a_ 1 seivkfnpvmasgfgayidhrdfleaktetiknllmrqgfvvvknldidsdtfrdiysay 60 d1o4ta_ 36 NKAR--LFARMKL------ppGSSVGLHKHE------GEFEIYYILLG-----eGVFHDN 76 :::: ::::::: :::::::::: ::::::::::: :::::: d1nx4a_ 61 GTIVerDTLKLEGekgkivtgRGQLPFHADGglllsqVDQVFLYAAEIknvkfrGATTVC 120 d1o4ta_ 77 ------------------------------------------------------------ 77 d1nx4a_ 121 dhalacqempahllrvleeetfevrvlwfkvpvftdlgwvrkmliyfpfdegqpaswepr 180 d1o4ta_ 77 -------------------------GKDVPIKAGDVCFTDSG-ESHSIENTGN--TDLEF 108 ::::::::::::::::: :::::::::: ::::: d1nx4a_ 181 ivgftdhetqaffqelgaflkqpryYYKHFWEDGDLLIMDNRrVIHEREEFNDddIVRRL 240 d1o4ta_ 109 LAVIILL 115 ::::::: d1nx4a_ 241 YRGQTAD 247 FAST alignment (Normalized score: 3.70 Raw score:623.40) d1o4ta_ 1 MVVRSSEITPERISNMRGGKGEVEMAHLLSKEAMH------------------------- 35 d1nx4a_ 1 -----------------------------------SEIVKFNPVMASGFGAYIDHRDFLE 25 d1o4ta_ 36 -----------------------------------NKAR--LFARMKLPPG--------- 49 :::: ::::::: d1nx4a_ 26 AKTETIKNLLMRQGFVVVKNLDIDSDTFRDIYSAYGTIVERDTLKLEG---EKGKIVTGR 82 d1o4ta_ 50 SSVGLHKHEG---------EFEIYYILLGE--------GVFHDN---------------- 76 ::::::: :::::::: :::: d1nx4a_ 83 GQLPFHA---DGGLLLSQVDQVFLYAA---EIKNVKFRGATT--VCDHALACQEMPAHLL 134 d1o4ta_ 77 ------------------------------------------------------------ 77 d1nx4a_ 135 RVLEEETFEVRVLWFKVPVFTDLGWVRKMLIYFPFDEGQPASWEPRIVGFTDHETQAFFQ 194 d1o4ta_ 77 -----------GKDVPIKAGDVCFT-DSGESHSI-ENTGN-TDLEFLAVIILL-- 115 :::::::::::::: :::::::: ::::: :::::::::: d1nx4a_ 195 ELGAFLKQPRYYYKHFWEDGDLLIMDNRRVIHEREEFNDDDIVRRLYRGQT--AD 247 TMalign alignment (TM-score: 0.56 Raw score:64.33) d1o4ta_ 1 ---------------------------------------------------------MVV 3 d1nx4a_ 1 SEIVKFNPVMASGFGAYIDHRDFLEAKTETIKNLLMRQGFVVVKNLDIDSDTFRDIY--- 57 d1o4ta_ 4 RSSEITPERISNMRGGKGEVEMAHLLSKEAM--HNKARL--FARMKLP------PGSSVG 53 : ::::: ::::::: :::::: d1nx4a_ 58 ------------------------------SAY-GTIVERDTLKLEGEKGKIVTGRGQLP 86 d1o4ta_ 54 LHKH------EGEFEIYYILLG--E---GVFHDN-------------------------- 76 :::: :::::::::::: : :::::: d1nx4a_ 87 FHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEMPAHLLRVLEEETFEVRV 146 d1o4ta_ 77 -----------------------------------------------------------G 77 : d1nx4a_ 147 LWFKVPVFTDLGWVRKMLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYY 206 d1o4ta_ 78 KDVPIKAGDVCFTDSG-ESHSIE-NTG-NTDLEFLAVIILL 115 :::::::::::::::: :::::: ::: ::::::::::::: d1nx4a_ 207 YKHFWEDGDLLIMDNRRVIHEREEFNDDDIVRRLYRGQTAD 247 HHsearch alignment (Probability: 0.01 E-value:0.25) d1o4ta_ 51 SVGLHK 56 :::::: d1nx4a_ 84 QLPFHA 89