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 | d1nnla_ | Phosphoserine phosphatase | HAD-like | HAD-like | α/β |
| Hit | d1dara2 | Elongation factor G (EF-G), N-terminal (G) domain | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 0.606 --> IntermediateDALI alignment (Z-score: 3.0 Raw score:421.70) query 1 dadeevysalvvglrAYVAknGFRSVLIGLSggiDSAL---------------------- 38 :::: :::::::::: :::: d1nnla_ 1 -----------selrKLFY--SADAVCFDVD---STVIreegidelakicgvedavpfka 44 query 39 -----------------------------vaAIACDALG--aqNVYGVSMPskyssdhSK 67 :::::::: :::::::: :: d1nnla_ 45 alterlaliqpsreqvqrliaeqpphltpgiRELVSRLQernvQVFLISGG-------FR 97 query 68 GDAAELARRTGL---NFRT------------------VSIEpmfdaymaslgltglaeen 106 :::::::::::: :::: :::: d1nnla_ 98 SIVEHVASKLNIpatNVFAnrlkfyfngeyagfdetqPTAE------------------- 138 query 107 lqsRLRGTTLMAISNQE----GHIVLAPGnkselavgystlyGDSV------gAYGPiKD 156 :::::::::::::: :::::::: :::: :::: :: d1nnla_ 139 ---SGGKGKVIKLLKEKfhfkKIIMIGDG------------aTDMEacppadaFIGF-GG 182 query 157 VYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaag 216 :: d1nnla_ 183 NV---------------------------------------------------------- 184 query 217 ydrelvvktlrmvdtaeykRRQY-PPGTkisakgfgkdrrlpitnrwregh 266 :::: :::: d1nnla_ 185 --------------irqqvKDNAkWYIT----------------dfvellg 205 FAST alignment (Normalized score: 1.83 Raw score:427.80) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGI-DSALVAAIACDALGAQN-VYGVSMP 58 :::::::: :::::: d1nnla_ 1 ----------------------------------SELRKLFYS---------ADAVCFD- 16 query 59 S----------------------------------------------------KYSSDHS 66 ::::::: d1nnla_ 17 -VDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGI 75 query 67 KGDAAELARRTGLNFRTVSIE--------------------------------------- 87 :::::::: ::::::::::: d1nnla_ 76 RELVSRLQ-ERNVQVFLISG-GFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDET 133 query 88 PMFDAYMASLGLTGLAEENLQS--RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLY 144 :::: :::::::::::::::: :::: d1nnla_ 134 QPTA------------------ESGGKGKVIKLLKEKFHFKKIIM--------------- 160 query 145 ---------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 195 :::::::: d1nnla_ 161 IGDGATDMEACPPADAF------------------------------------------- 177 query 196 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 255 d1nnla_ 178 ------------------------------------------------------------ 178 query 256 LPITNRWREGH---------------------------- 266 d1nnla_ 178 -----------IGFGGNVIRQQVKDNAKWYITDFVELLG 205 TMalign alignment (TM-score: 0.36 Raw score:94.46) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSA----------------------- 37 :::::::: : :::::::: ::::: d1nnla_ 1 -----------SELRKLFY-S-ADAVCFDV--DSTVIREEGIDELAKICGVEDAVPFKAA 45 query 38 --------------------------L-VAAIACDALGA-QNVYGVSMPSKYSSDHSKGD 69 : ::::::::::: ::::::::: : :::: d1nnla_ 46 LTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISG---G---FRSI 99 query 70 AAELARRTGLNFR-TV-S-------------IEPMF-DAYMASLGLTGLAEENLQSRLRG 113 ::::::::::::: :: : ::::: ::::::: d1nnla_ 100 VEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPT----------------AESGGKG 143 query 114 TTLMAISNQE-G-HIVLAPGNKSELAVGYSTLYGDSVG----AYGPIKDVYKTSIFRLAE 167 :::::::::: : ::::::: : : :::::: :::::: ::: d1nnla_ 144 KVIKLLKEKFHFKKIIMIGD---G------A-TDMEACPPADAFIGFG-GNV-------- 184 query 168 WRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLR 227 : : d1nnla_ 185 ----------------------------I--R---------------------------- 186 query 228 MVDTAEYKRRQYPPGTKI------SAKGFGKDRRLPITNRWREGH 266 : :: ::: ::::::: d1nnla_ 187 -Q--QV-KDN-AKWYITDFVELLG--------------------- 205 HHsearch alignment (Probability: 0.01 E-value:0.18) query 144 YGDSVGAYGPIK 155 :::::::::::: d1nnla_ 161 IGDGATDMEACP 172
Intermediate <-- 0.681 --> HitDALI alignment (Z-score: 2.2 Raw score:348.00) d1nnla_ 1 ------------------------------------------------------------ 1 d1dara2 1 mavkveydlkrlrnigiaahidagktttterilyytgraavttcfwkdhriniidtpghv 60 d1nnla_ 1 ---SELRKLFYSADAVCFDVDstvireegidelakicgvedavpfkaalterlaliqpsr 57 :::::::::::::::::: d1dara2 61 dftIEVERSMRVLDGAIVVFD--------------------------------------- 81 d1nnla_ 58 eqvqrliaeqpphlTPGIRELVSRLQERNVQVFLISGG------FRSIVEHVAS-KLNIP 110 :::::::::::::::::::::::: :::::::::: ::::: d1dara2 82 ---------ssqgvEPQSETVWRQAEKYKVPRIAFANKmdktgaDLWLVIRTMQeRLGAR 132 d1nnla_ 111 AT---------------------------------------------------------- 112 :: d1dara2 133 PVvmqlpigredtfsgiidvlrmkaytygndlgtdireipipeeyldqareyheklveva 192 d1nnla_ 113 ------------------------------------NVFAnrlkfyfngeyagfdetqpT 136 :::: : d1dara2 193 adfdenimlkylegeepteeelvaairkgtidlkitPVFL-------------------G 233 d1nnla_ 137 AES--GGKGKVIKLLKeKFHFKkiimigdgatdmeacppadafigfggnvirqqvkdnak 194 ::: ::::::::::: ::::: d1dara2 234 SALknKGVQLLLDAVV-DYLPS-------------------------------------- 254 d1nnla_ 195 wyitdfvellg 205 d1dara2 255 ----------- 255 FAST alignment (Normalized score: 2.56 Raw score:584.10) d1nnla_ 1 ------------------------------------------------------------ 1 d1dara2 1 MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRAAVTTCFWKDHRINIIDTPGHV 60 d1nnla_ 1 ---SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSR 57 :::::::::::::::: d1dara2 61 DFTIEVERSMRVLDGAIVV----------------------------------------- 79 d1nnla_ 58 EQVQRLIAEQPP-----HLTPGIRELVSRLQERNVQVFLISG--------GFRSIVEHVA 104 ::::::::::::::::::::::: :::::::::: d1dara2 80 ------------FDSSQGVEPQSETVWRQAEKYKVPRIAF--ANKMDKTGADLWLVIRTM 125 d1nnla_ 105 -SKLNIPAT--------------------------------------------------- 112 :::::: d1dara2 126 QERLGAR--PVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQARE 183 d1nnla_ 113 ---------------------------------------------NVFANRLKFYFNGEY 127 :::: d1dara2 184 YHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFL----------- 232 d1nnla_ 128 AGFDETQPTAES---------GGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFI 178 ::::::::: d1dara2 233 ------------GSALKNKGVQLLLDAVVD------------------------------ 250 d1nnla_ 179 GFGGNVIRQQVKDNAKWYITDFVELLG---- 205 d1dara2 251 ---------------------------YLPS 254 TMalign alignment (TM-score: 0.33 Raw score:67.05) d1nnla_ 1 --------SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLAL 52 d1dara2 1 MAVKVEYD---------------------------------------------------- 8 d1nnla_ 53 IQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLIS-GG-FRSIVEHVASKLNI- 109 ::::::::::: :: :::::::::::::: d1dara2 9 ------------------------------LKRLRNIGIAAHIDAGKTTTTERILYYTGR 38 d1nnla_ 110 PATN------------VFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKK 157 ::: ::: ::: ::: ::::::::: : : d1dara2 39 -AAVTTCFWKDHRINIIDT------------------PGH-VDF-TIEVERSMR-V-L-- 73 d1nnla_ 158 IIMIG-D-----G----ATDMEACPPADAFIGFGGN--------V--IRQQVKD--NA-- 193 ::::: : : ::::::::::::::::::: : ::::::: :: d1dara2 74 DGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARP 133 d1nnla_ 194 ------------------------------------------------------------ 194 d1dara2 134 VVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAA 193 d1nnla_ 194 --------------------------------KWYITD------------F-VEL-LG-- 205 :::::: : ::: :: d1dara2 194 DFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLP 253 d1nnla_ 206 - 206 d1dara2 254 S 254 HHsearch alignment (Probability: 0.02 E-value:0.11) d1nnla_ 66 EQPPHLTPGIRELVSRLQERNVQVFLISGGFRSI 99 :::::::::::::::::::::::::::::::::: d1dara2 81 DSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKT 114