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 | d1vj2a_ | Hypothetical protein TM1459 | RmlC-like cupins | Double-stranded beta-helix | All β |
| Hit | d1pg6a_ | Hypothetical protein SPyM3 0169 (SPyM18 0222, SPS0176) | TRAP-like | Double-stranded beta-helix | All β |
Query <-- 1.662 --> IntermediateDALI alignment (Z-score: 11.8 Raw score:636.30) query 1 meinadftkPVVIDTDQLEWRPSP---MKGVERRMLDRIGgevaRATSIVRYAPGSRFSA 57 ::::::::::::::: ::::::::::::: :::::::::::::::: d1vj2a_ 1 ---------MILKRAYDVTPQKIStdkVRGVRKRVLIGLKdapnFVMRLFTVEPGGLIDR 51 query 58 HTHDGGEEFIVLDGVFQDE----HGDYPAGTYVRNPPTTSHVPGSAE--GCTIFVKLWQF 111 ::::::::::::::::::: :::::::::::::::::::::::: ::::::::::: d1vj2a_ 52 HSHPWEHEIFVLKGKLTVLkeqgEETVEEGFYIFVEPNEIHGFRNDTdsEVEFLCLIPKE 111 query 112 dpadrtqfsknm 123 d1vj2a_ 112 ---------gge 114 FAST alignment (Normalized score: 9.80 Raw score:1161.00) query 1 MEINADFTKPVVIDTDQLEWRPS----PMKGVERRMLDRIGGEVA-------RATSIVRY 49 ::::::::::::: ::::::::::: :::::::: d1vj2a_ 1 ---------MILKRAYDVTPQK-ISTDKVRGVRKRVLI-------GLKDAPNFVMRLFTV 43 query 50 APGSRFSAHTHDGGEEFIVLDGVFQDE-----HGDYPAGTYVRNPPTTSHVPGS--AEGC 102 :::::::::::::::::::::::::: :::::::::::::::::::::: :::: d1vj2a_ 44 EPGGLIDRHSHPWEHEIFVLKGKLTV-LKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEV 102 query 103 TIFVKLWQFDPADRTQFSKNM----- 123 ::::::: d1vj2a_ 103 EFLCLIP--------------KEGGE 114 TMalign alignment (TM-score: 0.68 Raw score:83.64) query 1 MEINADFTKPVVIDTDQLEWRPSP---MKGVERRMLDRIG----GEVARATSIVRYAPGS 53 ::::::::::::::: ::::::::::::: :::::::::::: d1vj2a_ 1 ---------MILKRAYDVTPQKISTDKVRGVRKRVLIGLKDAPN----FVMRLFTVEPGG 47 query 54 RFSAHTHDGGEEFIVLDGVFQD----EHGDYPAGTYVRNPPTTSHVPGSAE--GCTIFVK 107 :::::::::::::::::::::: ::::::::::::::::::::::::: ::::::: d1vj2a_ 48 LIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCL 107 query 108 LWQF---DPADRTQFSKNM 123 :::: d1vj2a_ 108 IPKEGGE------------ 114 HHsearch alignment (Probability: 0.97 E-value:0.00) query 13 IDTDQLEWRPSPMKGVERRMLDRIGGEVARATSIVRYAPGSRFSAHTHDGGEEFIVLDGV 72 :::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: d1vj2a_ 9 VTPQKISTDK--VRGVRKRVLIGLKDAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGK 66 query 73 ----FQDEHGDYPAGTYVRNPPTTSHVPGS--AEGCTIFV 106 :::::::::::::::::::::::::: :::::::: d1vj2a_ 67 LTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLC 106
Intermediate <-- 1.166 --> HitDALI alignment (Z-score: 2.5 Raw score:264.00) d1vj2a_ 1 milkraydvtpqkistdkvrGVRKRVLIglkdapnFVMRLFTVEPGGLIDrhshpweHEI 60 :::::::: ::::::::::::::: ::: d1pg6a_ 1 --------------------RMRFTIDQ----nmqFPLVEIDLEHGGSVY---lqqgSMV 33 d1vj2a_ 61 FVlKGKLTVLKEQG----eetveegfyifvepNEIHGFRNDTdsEVEFLCLIPKEGGE-- 114 :: ::::::::::: :::::::::: :::::::::::::: d1pg6a_ 34 YH-TENVTLNTKLNglgklvgaigrsmvsgesMFITQAMSNG--DGKLALAPNTPGQIva 90 d1vj2a_ 115 ------------------------------------------------------------ 115 d1pg6a_ 91 lelgekqyrlndgaflaldgsaqykmerqniggglfvmtteglgtllansfgsikkitld 150 d1vj2a_ 115 ------------------------------------------------------------ 115 d1pg6a_ 151 ggtmtidnahvvawsreldydihlengfmqsigtgegvvntfrghgeiyiqslnleqfag 210 d1vj2a_ 115 ------ 115 d1pg6a_ 211 tlkryl 216 FAST alignment (Normalized score: 2.41 Raw score:377.80) d1vj2a_ 1 MILKRAYDVTPQKISTDKVRGVRKRVLIGLKDAPNFVMRLFTVEPGGLIDRHSHPWEHEI 60 :::::: ::::: :::::::::::::: d1pg6a_ 1 --------------------RMRFTI---DQNMQ-FPLVEIDLEHGGSV----------- 25 d1vj2a_ 61 FV---------LKGKLTVLKEQGEETVEEGFYIFVEPN---------------------E 90 :::::::::: : d1pg6a_ 26 --YLQQGSMVYHTENVTLNTK-----------------LNGLGKLVGAIGRSMVSGESMF 66 d1vj2a_ 91 IHGFRNDTD-SEVEFLCLIPKEGGE----------------------------------- 114 :::::: ::::::::: d1pg6a_ 67 ITQAMS---NGDGKLALAP------NTPGQIVALELGEKQYRLNDGAFLALDGSAQYKME 117 d1vj2a_ 115 ------------------------------------------------------------ 115 d1pg6a_ 118 RQNIGGGLFVMTTEGLGTLLANSFGSIKKITLDGGTMTIDNAHVVAWSRELDYDIHLENG 177 d1vj2a_ 115 --------------------------------------- 115 d1pg6a_ 178 FMQSIGTGEGVVNTFRGHGEIYIQSLNLEQFAGTLKRYL 216 TMalign alignment (TM-score: 0.48 Raw score:55.15) d1vj2a_ 1 MILKRAYDVTPQKISTDKVRGVRKRVLIGLKDAPNFVMRLFTVEPGGLIDRHSHPWEHEI 60 ::::::::: :: ::::::::::::::: ::: :::: d1pg6a_ 1 --------------------RMRFTIDQN--MQ--FPLVEIDLEHGGSVY-LQQ--GSMV 33 d1vj2a_ 61 FVLKGKLTVLKEQG------------------EETVEEGFYIFVEPNEIHGFRNDTDSEV 102 :: ::::::::::: :::::::: : ::: d1pg6a_ 34 YH-TENVTLNTKLNGLGKLVGAIGRSMVSGES--------------MFITQAMS-N-GDG 76 d1vj2a_ 103 EFLCLI-P-KE----------------G-------------------------------- 112 :::::: : :: : d1pg6a_ 77 KLALAPNTPGQIVALELGEKQYRLNDGAFLALDGSAQYKMERQNIGGGLFVMTTEGLGTL 136 d1vj2a_ 113 --GE-------------------------------------------------------- 114 :: d1pg6a_ 137 LANSFGSIKKITLDGGTMTIDNAHVVAWSRELDYDIHLENGFMQSIGTGEGVVNTFRGHG 196 d1vj2a_ 115 -------------------- 115 d1pg6a_ 197 EIYIQSLNLEQFAGTLKRYL 216 HHsearch alignment (Probability: 0.03 E-value:0.17) d1vj2a_ 42 T 42 : d1pg6a_ 18 D 18