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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1a9xa1 | Carbamoyl phosphate synthetase, large subunit connection domain | Carbamoyl phosphate synthetase, large subunit connection domain | Carbamoyl phosphate synthetase, large subunit connection domain | All α |
| Hit | d1g2ha_ | Transcriptional regulator TyrR, C-terminal domain | Homeodomain-like | DNA/RNA-binding 3-helical bundle | All α |
Query <-- 0.803 --> IntermediateDALI alignment (Z-score: 3.0 Raw score:188.40) query 1 dadeevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpsk 60 d1a9xa1 1 ------------------------------------------------------------ 1 query 61 yssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmais 120 d1a9xa1 1 ------------------------------------------------------------ 1 query 121 nqeghivlapgNKSElavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtp 180 :::: d1a9xa1 1 -------evgaTGFD----------------------------------pkvslddpeal 19 query 181 pipeasitkpdyPVLDAILELYVdRDTGADAIVAAG-YDRELVVKTLRMVDTA-EYKRRQ 238 ::::::::::: :::::::::::: :::::::::::::::: :::::: d1a9xa1 20 tkirrelkdagaDRIWYIADAFR-AGLSVDGVFNLTnIDRWFLVQIEELVRLEeKVAEVG 78 query 239 -------------------------YPPGT----------------------kisakgfg 251 ::::: d1a9xa1 79 itglnadflrqlkrkgfadarlaklAGVREaeirklrdqydlhpvykrvdtcaaefatdt 138 query 252 kdrrlpitnrwregh 266 d1a9xa1 139 aymystyeeeceanp 153 FAST alignment (Normalized score: 1.04 Raw score:209.40) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 d1a9xa1 1 ------------------------------------------------------------ 1 query 61 YSSDHSKGDAAELARRTGLNFRTVSIE--------------------------------- 87 d1a9xa1 1 ---------------------------EVGATGFDPKVSLDDPEALTKIRRELKDAGADR 33 query 88 -----------PMFDAYMASLGLTGL-AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSE 135 ::::::::::: :::::::::::::::::::: d1a9xa1 34 IWYIADAFRAGLSVDGVFNLTN----IDRWFLVQIEELVRLEEKVAE------------- 76 query 136 LAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 195 d1a9xa1 77 ------------------------------------------------------------ 77 query 196 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 255 d1a9xa1 77 ------------------------------------------------------------ 77 query 256 LPITNRWREGH------------------------------------------------- 266 d1a9xa1 77 -----------VGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYK 125 query 267 ---------------------------- 267 d1a9xa1 126 RVDTCAAEFATDTAYMYSTYEEECEANP 153 TMalign alignment (TM-score: 0.24 Raw score:64.36) query 1 --------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDA 46 :::::::::: ::: : d1a9xa1 1 EVGATGFDPKVSLD-----DPEALTKIRR-----------------------ELK-D--- 28 query 47 LGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEEN 106 : d1a9xa1 29 -------A---------------------------------------------------- 29 query 107 LQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYK-TSIFRL 165 :::::: ::::::: :::::: d1a9xa1 30 --------------------GADRIW--------------------YIADAFRAGLSVDG 49 query 166 AEWRNRAAAERGQTPPIPEASITK--PDY-PVLDAILELYVDRDT--GADAIVAAGYDRE 220 :: : ::: :::: :: :::::::::: :::: ::: : : d1a9xa1 50 VF--N----------LTN--IDRWFL-VQIEELVRLEEKV-AEVGITGLN--A-----D- 85 query 221 LVVKTLR--MVDTAEYKR-RQYPPGTKISAKGFG-KDRRLPITNRWRE-GH--------- 266 :::::: :::: : : ::: ::::::::::: :: d1a9xa1 86 -FLRQLKRKGFAD-A--RL------------AKLA--GVREAEIRKLRDQYDLHPVYKRV 127 query 267 -------------------------- 267 d1a9xa1 128 DTCAAEFATDTAYMYSTYEEECEANP 153 HHsearch alignment (Probability: 0.03 E-value:0.25) query 197 AILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAE 233 :::::::::::::::::: ::::::::::::::::::: d1a9xa1 35 WYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEE 72
Intermediate <-- 0.988 --> HitDALI alignment (Z-score: 4.9 Raw score:173.00) d1a9xa1 1 evgatgfdpkvslddpealtkirrelkdagadriwyiadafraglsvdgvfnltnidrwf 60 d1g2ha_ 1 ------------------------------------------------------------ 1 d1a9xa1 61 lvqieelvRLEEKVAEVGITG----lNADFLRQLKRKGFADARLAKLAGVREAEIRKLRD 116 ::::::::::::: :::::::::::::::::::::::::::::::::: d1g2ha_ 1 -----savISLDEFENKTLDEiigfyEAQVLKLFYAEYPSTRKLAQRLGVSHTAIANKLK 55 d1a9xa1 117 QYDLHPvykrvdtcaaefatdtaymystyeeeceanp 153 :::::: d1g2ha_ 56 QYGIGK------------------------------- 61 FAST alignment (Normalized score: 3.79 Raw score:366.60) d1a9xa1 1 EVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWF 60 d1g2ha_ 1 ------------------------------------------------------------ 1 d1a9xa1 61 LVQIEELVR----LEEKVAEVG-ITGL---NADFLRQLKRKG--FADARLAKLAGVREAE 110 ::::::::: :::: :::::::::: :::::::::::::::: d1g2ha_ 1 ---------SAVISLDEFENKTLDEIIGFYEAQVLKLFYA--EYPSTRKLAQRLGVSHTA 49 d1a9xa1 111 IRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEECEANP--- 153 ::::::::: d1g2ha_ 50 IANKLKQYG----------------------------------IGK 61 TMalign alignment (TM-score: 0.28 Raw score:43.02) d1a9xa1 1 ----EVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNI 56 d1g2ha_ 1 SAVI-------------------------------------------------------- 4 d1a9xa1 57 DRWFLVQIEELVRLEEKVAEVG-IT-GL---NADFLRQLKRKGF-ADARLAKLAGVREAE 110 :: ::::: : :: :: ::::::::::: : ::::::::::::::: d1g2ha_ 5 ------------SL-DEFEN-KTLDEIIGFYEAQVLKLFYAE-YPSTRKLAQRLGVSHTA 49 d1a9xa1 111 IRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEECEANP 153 :::::::::::: d1g2ha_ 50 IANKLKQYGIGK------------------------------- 61 HHsearch alignment (Probability: 0.11 E-value:0.03) d1a9xa1 96 ADARLAKLAGVREAEIRKLRDQYDLH 121 :::::::::::::::::::::::::: d1g2ha_ 35 STRKLAQRLGVSHTAIANKLKQYGIG 60