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 | d2ptha_ | Peptidyl-tRNA hydrolase | Peptidyl-tRNA hydrolase-like | Phosphorylase/hydrolase-like | 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 <-- 1.509 --> HitDALI alignment (Z-score: 2.7 Raw score:348.00) d1nnla_ 1 selrklfySADAVCFDV----------DSTVireegidelakicgvedavpfkaalterl 50 ::::::::: :::: d2ptha_ 1 --------TIKLIVGLAnpgaeyaatrHNAG----------------------------- 23 d1nnla_ 51 aliqpsreqvqrliaeqpphltpgIRELVSR----------------LQER---NVQVFL 91 ::::::: :::: :::::: d2ptha_ 24 ---------------------awfVDLLAERlraplreeakffgytsRVTLggeDVRLLV 62 d1nnla_ 92 IsggfrsivehvasklnipatnvFANRlkfyfngeyagfdetqptaesGGKGKVIKLLKE 151 : :::: :::::::::::: d2ptha_ 63 P----------------------TTFM---------------------NLSGKAVAAMAS 79 d1nnla_ 152 KFHFK--KIIMIGD------------------gATDME-ACPP-----aDAFIGFGgnVI 185 ::::: ::::::: ::::: :::: ::::::: :: d2ptha_ 80 FFRINpdEILVAHDeldlppgvakfklggghggHNGLKdIISKlgnnpnFHRLRIG--IG 137 d1nnla_ 186 RQ-------------qvkdnakwyitDFVELLG----------------------- 205 :: ::::::: d2ptha_ 138 HPgdknkvvgfvlgkppvseqklideAIDEAARctemwftdgltkatnrlhafkaq 193 FAST alignment (Normalized score: 1.17 Raw score:233.00) d1nnla_ 1 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSREQV 60 d2ptha_ 1 ------------------------------------------------------------ 1 d1nnla_ 61 QRLIAEQPPHL------------------------------------------------- 71 d2ptha_ 1 -----------TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTS 49 d1nnla_ 72 -----------------TPGIRELVSRLQER-------NVQVFLISGGFRSIV------- 100 ::::::::::::: :::::::: d2ptha_ 50 RVTLGGEDVRLLVPTTFMNLSGKAVAAMAS-FFRINPDEILVAHDE-------LDLPPGV 101 d1nnla_ 101 -----------EHVASKLNIPATN---------------VFANRLKFYFNGEYAGFDETQ 134 :::::: :::::: d2ptha_ 102 AKFKLGGGHGGHNGLKD-------IISKLGNNPNFHRLRIGIGHP--------------- 139 d1nnla_ 135 PTA-----------------ESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAF 177 ::::::::::::::: d2ptha_ 140 ---GDKNKVVGFVLGKPPVSEQKLIDEAIDEAARC------------------------- 171 d1nnla_ 178 IGFGGNVIRQQVKDNAKWYITDFVELLG---------------------- 205 d2ptha_ 172 ----------------------------TEMWFTDGLTKATNRLHAFKAQ 193 TMalign alignment (TM-score: 0.28 Raw score:56.48) d1nnla_ 1 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAV----PFKAA----------- 45 : ::::::: : :: :::: : d2ptha_ 1 -------T----IKLIVGL-----A-NP--------GAEYAATR----HNAGAWFVDLLA 31 d1nnla_ 46 --------LTERLALIQPSREQVQRLIAEQPPHLTPGI-RELVS-------RLQERNVQV 89 :::::::::::::: ::::: d2ptha_ 32 ERLRAPLR----------------EEAKFFGYTSRVTLGGEDVRLLVPTTF--------- 66 d1nnla_ 90 FLISGGFRSIVEHVASKLNIPATNVFA------------------NRLKFYFNGEYAGFD 131 :::::::::::::::::::::::: d2ptha_ 67 ---MNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGG--------------- 108 d1nnla_ 132 ETQPTAESGGK--GKVI-----KLLKEKFHFKKIIMIGDGATDME--------------- 169 :::::::: :: :: : ::::: ::: :: d2ptha_ 109 ---GHGGHNGLKD--IISKLGN-----NP-N--FHRLR-IGI-GHPGDKNKVVGFVLGKP 153 d1nnla_ 170 ----ACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLG---------------- 205 :::::::::::::::::::: d2ptha_ 154 PVSE----------------QKLIDEAIDEAARCTEMWFTDGLTKATNRLHAFKAQ 193 HHsearch alignment (Probability: 0.01 E-value:0.17) d1nnla_ 136 TAESGGKGKVIKLLKEKFHFKKIIMIGDG 164 ::::::::::::::::::::::::::::: d2ptha_ 66 FMNLSGKAVAAMASFFRINPDEILVAHDE 94