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 | d1j1la_ | Pirin | RmlC-like cupins | Double-stranded beta-helix | All β |
| Hit | d1nlqa_ | Chromatin decondensation protein 1 (Crp1, Nlp) | Nucleoplasmin-like core domain | Nucleoplasmin-like/VP (viral coat and capsid proteins) | All β |
Query <-- 1.062 --> IntermediateDALI alignment (Z-score: 9.2 Raw score:663.80) query 1 meinadfTKPVVIDtdqLEWRPSpMKGVERRMLDR----IGGEVARATSIVRYAPGSRFS 56 ::::::: :::::: ::::::::::: ::::::::::::::::::::: d1j1la_ 1 ----sskKVTLSVL---SREQSE-GVGARVRRSIGrpelKNLDPFLLFDEFKGGRPGGFP 52 query 57 AHTHD-GGEEFIVL-DGVFQDE-----HGDYPAGTYVRNPP--TTSHVPGSAE--GCTIF 105 ::::: :::::::: ::::::: :::::::::::::: :::::::::: ::::: d1j1la_ 53 DHPHRgFETVSYLLeGGSMAHEdfcghTGKMNPGDLQWMTAgrGILHAEMPCSeePAHGL 112 query 106 VKLWQF---DPAD-RTQFSKNM-------------------------------------- 123 :::::: :::: :::::::: d1j1la_ 113 QLWVNLrssEKMVePQYQELKSeeipkpskdgvtvavisgealgikskvytrtptlyldf 172 query 124 ------------------------------------------------------------ 124 d1j1la_ 173 kldpgakhsqpipkgwtsfiytisgdvyigpddaqqkiephhtavlgegdsvqvenkdpk 232 query 124 -------------------------------------------------------- 124 d1j1la_ 233 rshfvliageplrepviqhgpfvmntneeisqaildfrnakngferaktwkskign 288 FAST alignment (Normalized score: 5.54 Raw score:1043.00) query 1 MEINADFTK-----PVVIDTDQLEWRPSPMKGVERRMLDRIGGEV-----------ARAT 44 ::::: ::::: :::::::::: :::: d1j1la_ 1 ---------SSKKVTLSVL---SREQS-EGVGARVRRS-------IGRPELKNLDPFLLF 40 query 45 SIVRYAPGS--RFSAHTHD-GGEEFIVL-DGVFQDE-------HGDYPAGTYVRNPP--- 90 ::::::: :::::::: :::::::: ::::: :::::::::::: d1j1la_ 41 DEFKGGR--PGGFPDHPHRGFETVSYLLEGGSMA--HEDFCGHTGKMNPGDLQWM--TAG 94 query 91 -TTSHVPGS--AEGCTIFVKLWQF-------DPAD-RTQFSKNM---------------- 123 :::::::: ::::::::: :::: :::::: d1j1la_ 95 RGILHAEMPCSEEPAHGLQL----WVNLRSSEKMVEPQYQEL--KSEEIPKPSKDGVTVA 148 query 124 ------------------------------------------------------------ 124 d1j1la_ 149 VISGEALGIKSKVYTRTPTLYLDFKLDPGAKHSQPIPKGWTSFIYTISGDVYIGPDDAQQ 208 query 124 ------------------------------------------------------------ 124 d1j1la_ 209 KIEPHHTAVLGEGDSVQVENKDPKRSHFVLIAGEPLREPVIQHGPFVMNTNEEISQAILD 268 query 124 -------------------- 124 d1j1la_ 269 FRNAKNGFERAKTWKSKIGN 288 TMalign alignment (TM-score: 0.59 Raw score:72.48) query 1 ---------------------------------------------------------MEI 3 d1j1la_ 1 SSKKVTLSVLSREQSEGVGARVRRSIGRPELKNLDPFLLFDEFKGGRPGGFPDHPHR--- 57 query 4 NADFTKPVVIDTD-----------------QL---------------------------- 18 :::::::::: :: d1j1la_ 58 ---GFETVSYLLEGGSMAHEDFCGHTGKMNPGDLQWMTAGRGILHAEMPCSEEPAHGLQL 114 query 19 -------------------E---WRPSPMKGVERRMLDR---------IG--GEVARATS 45 : :::: ::::::::::: :: ::::: d1j1la_ 115 WVNLRSSEKMVEPQYQELKSEEIPKPS-KDGVTVAVISGEALGIKSKVYTRT---PTLYL 170 query 46 IVRYAPGSRFSAHTH-D-GGEEFIVLDGVFQD----EHGDYPAGTYVRNPPTTSHVPGSA 99 :::::::::: :::: : :::::::::::::: :::::::::::::::::::::::: d1j1la_ 171 DFKLDPGAKH-SQPIPKGWTSFIYTISGDVYIGPDDAQQKIEPHHTAVLGEGDSVQVENK 229 query 100 E--GCTIFVKLWQFDPA------------------------------------------- 114 : :::::::: ::::: d1j1la_ 230 DPKRSHFVLIA-GEPLREPVIQHGPFVMNTNEEISQAILDFRNAKNGFERAKTWKSKIGN 288 query 115 DRTQFSKNM 123 d1j1la_ 289 --------- 289 HHsearch alignment (Probability: 0.84 E-value:0.00) query 28 VERRMLDRIGGEVARATSIVRYAPGSR--FSAHTHDGGEEF-IVLD-GVF-----QDEHG 78 ::::::::::::::::::::::::::: :::::::::::: :::: ::: ::::: d1j1la_ 22 VRRSIGRPELKNLDPFLLFDEFKGGRPGGFPDHPHRGFETVSYLLEGGSMAHEDFCGHTG 81 query 79 DYPAGTYVRNPPTT 92 :::::::::::::: d1j1la_ 82 KMNPGDLQWMTAGR 95
Intermediate <-- 0.801 --> HitDALI alignment (Z-score: 5.6 Raw score:342.40) d1j1la_ 1 sskkvtlsvlsreqsegvgarvrrsigrpelknldpfllfdefkggrpggfpdhphrgfe 60 d1nlqa_ 1 ------------------------------------------------------------ 1 d1j1la_ 61 tvsylleggsmahedfcghtgkmnpgdlqwmtagrgilhaempcseepahglqlwvnlrs 120 d1nlqa_ 1 ------------------------------------------------------------ 1 d1j1la_ 121 sekmvepqyqelkseeipkpskdgvtvavisgealgikskvytrtPTLYLDFKLDP-GAK 179 ::::::::::: ::: d1nlqa_ 1 ---------------------------------------------EESFYGVTLTAeSDS 15 d1j1la_ 180 HSQPIP----KGWTSFIYTISG----------DVYIGPD--DAQQKIE---------PHH 214 :::::: :::::::::::: ::::::: ::::::: ::: d1nlqa_ 16 VTWDVDedyaRGQKLVIKQILLgaeakenefnVVEVNTPkdSVQIPIAvlkagetraVNP 75 d1j1la_ 215 TAVLGEGdSVQVENKDP-KRSHFVLIAGEPlrepviqhgpfvmntneeisqaildfrnak 273 ::::::: ::::::::: :::::::::::: d1nlqa_ 76 DVEFYES-KVTFKLIKGsGPVYIHGHNIKD------------------------------ 104 d1j1la_ 274 ngferaktwkskign 288 d1nlqa_ 105 --------------d 105 FAST alignment (Normalized score: 2.89 Raw score:502.40) d1j1la_ 1 SSKKVTLSVLSREQSEGVGARVRRSIGRPELKNLDPFLLFDEFKGGRPGGFPDHPHRGFE 60 d1nlqa_ 1 ------------------------------------------------------------ 1 d1j1la_ 61 TVSYLLEGGSMAHEDFCGHTGKMNPGDLQWMTAGRGILHAEMPCSEEPAHGLQLWVNLRS 120 d1nlqa_ 1 ------------------------------------------------------------ 1 d1j1la_ 121 SEKMVEPQYQELKSEEIPKPSKDGVTVAVISGEALGIKSKVYTRTPTLYLDFKLDPG-AK 179 :::::::::::: :: d1nlqa_ 1 ---------------------------------------------EESFYGVTLTAESDS 15 d1j1la_ 180 HSQPIP----KGWTSFIYTIS--------------GDVYIGPD-----DAQQKIE----- 211 :::::: ::::::: ::::: ::::: d1nlqa_ 16 VTWDVDEDYARGQKLVI----KQILLGAEAKENEFNVVEV---NTPKDSVQIP--IAVLK 66 d1j1la_ 212 ------PHHTAVLGEGDSVQVENK-DPKRSHFVLIAGEPLREPVIQHGPFVMNTNEEISQ 264 ::::::::: :::::::: :::::::::::::: d1nlqa_ 67 AGETRAVNPDVEFYE-SKVTFKLIKGSGPVYIHGHNIKD--------------------- 104 d1j1la_ 265 AILDFRNAKNGFERAKTWKSKIGN- 288 d1nlqa_ 105 ------------------------D 105 TMalign alignment (TM-score: 0.25 Raw score:71.28) d1j1la_ 1 SSKKVTLSVLSREQSEGVGARVRRSIGRPELKNLDPFLLFDEFKGGRPGGFPDHPH---- 56 ::::::::::::::::: ::: d1nlqa_ 1 -----------------------------------EESFYGVTLTAESDSVT-WDVDEDY 24 d1j1la_ 57 --RGFETVSYLLE---G-----GSMAHEDF-CGHTGK-MNP------GDLQWMTAGRGIL 98 ::::::::::: : :::::::: :::::: ::: ::::::::: ::: d1nlqa_ 25 ARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFY-ESK 83 d1j1la_ 99 HAEMPCSEEPAHGLQLWVNLRSSEKMVEPQYQELKSEEIPKPSKDGVTVAVISGEALGIK 158 ::::::::::::::::::: d1nlqa_ 84 VTFKLIKGSGPVYIHGHNI----------------------------------------- 102 d1j1la_ 159 SKVYTRTPTLYLDFKLDPGAKHSQPIPKGWTSFIYTISGDVYIGPDDAQQKIEPHHTAVL 218 d1nlqa_ 103 ------------------------------------------------------------ 103 d1j1la_ 219 GEGDSVQVENKDPKRSHFVLIAGEPLREPVIQHGPFVMNTNEEISQAILDFRNAKNGFER 278 ::: d1nlqa_ 103 ------------------------------------KDD--------------------- 105 d1j1la_ 279 AKTWKSKIGN 288 d1nlqa_ 106 ---------- 106 HHsearch alignment (Probability: 0.04 E-value:0.49) d1j1la_ 168 LYLDFKLDPG-AKHSQPIP 185 :::::::::: :::::::: d1nlqa_ 3 SFYGVTLTAESDSVTWDVD 21