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 | d1im5a_ | Pyrazinamidase/nicotinamidase | Isochorismatase-like hydrolases | Isochorismatase-like hydrolases | α/β |
| Hit | d1rkqa_ | Hypothetical protein YidA | HAD-like | HAD-like | α/β |
Query <-- 0.845 --> IntermediateDALI alignment (Z-score: 2.3 Raw score:295.90) query 1 ------------------------------------------------------------ 1 d1im5a_ 1 peealivvdmqrdfmpggalpvpegdkiipkvneyirkfkekgalivatrdwhpenhisf 60 query 1 -------------------------------------DADE-evYSALvvGLRAYVAKNG 22 :::: :::: :::::::::: d1im5a_ 61 rerggpwprhcvqntpgaefvvdlpedaviiskatepDKEAysgFEGT--DLAKILRGNG 118 query 23 FRSVLIG-lsGGIDSALVAAIACDALGaqNVYGVSMpskySSDHSKGDAAELARRTGLNF 81 ::::::: ::::::::::::::::: ::::::: :::::::::::::::::::: d1im5a_ 119 VKRVYICgvaTEYCVRATALDALKHGF--EVYLLRDavkgIKPEDEERALEEMKSRGIKI 176 query 82 RTVsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgys 141 ::: d1im5a_ 177 VQF--------------------------------------------------------- 179 query 142 tlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailel 201 d1im5a_ 180 ------------------------------------------------------------ 180 query 202 yvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnr 261 d1im5a_ 180 ------------------------------------------------------------ 180 query 262 wregh 266 d1im5a_ 180 ----- 180 FAST alignment (Normalized score: 2.15 Raw score:469.10) query 1 DADEEVYSALV------------------------------------------------- 11 d1im5a_ 1 -----------PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVAT 49 query 12 ----------------------------------------------------------VG 13 :: d1im5a_ 50 RDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSGFEGTD 109 query 14 LRAYVAKNGFRSVLIGLS----GGIDSALVAAIACDALGAQ---NVYGVSMPSKY----- 61 ::::::::::::::: :::::::::::::: ::::: d1im5a_ 110 LAKILRGNGVKRVYI---CGVATEYCVRATALDALK-----HGFEVYLL------RDAVK 155 query 62 -SSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAIS 120 ::::::::::::::::::::: d1im5a_ 156 GIKPEDEERALEEMKSRGIKIV-------------------------------------- 177 query 121 NQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTP 180 d1im5a_ 178 ------------------------------------------------------------ 178 query 181 PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYP 240 d1im5a_ 178 ------------------------------------------------------------ 178 query 241 PGTKISAKGFGKDRRLPITNRWREGH-- 266 d1im5a_ 178 --------------------------QF 179 TMalign alignment (TM-score: 0.30 Raw score:81.01) query 1 --------------DADE------EVYSALVVGLRAYVAKN-G-FRSVLIGLSGG----- 33 ::: ::: ::::::::::::: : ::::::::::: d1im5a_ 1 PEEALIVVDMQRDF-MPGGALPVPEGD-KIIPKVNEYIRKFKEKGALIVATRDWHPENHI 58 query 34 -----------ID-SA---LVAAIACDALGAQNVYGVSMPSKYSSDHSK---GDAAELAR 75 :: : :::::: ::: :::::::: :::::: d1im5a_ 59 SFRERGGPWPRHCV-QNTPGAEFVV--DLP-EDAVIISK----ATEPDKEAY-------- 102 query 76 RTGLNFRTVSIEPMFDAYMASLGLTGLAEEN-LQSRLRGTTLMAISNQ--EGHIVLAPGN 132 : ::::::::::::::: ::::::: d1im5a_ 103 ------------------------------SG-FEGTDLAKILRGNGVKR---VYICGVA 128 query 133 KSELAVGYSTLYGDS---V-GAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASIT 188 :::: ::::::::: : ::::::::::: d1im5a_ 129 TEYC--VRATALDALKHGFEVYLLRDAVKGI----------------------------- 157 query 189 KPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 248 :: :: :: : :::::::: ::::::: d1im5a_ 158 -------KP-ED-EE----------------------R-ALEEMKSR-GIKIVQF----- 179 query 249 GFGKDRRLPITNRWREGH 266 d1im5a_ 180 ------------------ 180 HHsearch alignment (Probability: 0.10 E-value:0.05) query 13 GLRAYVAKNGFRSVLIGL---SGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGD 69 :::::::::::::::::: ::::::::::::: :::: :::::::::::::::::: d1im5a_ 109 DLAKILRGNGVKRVYICGVATEYCVRATALDALK---HGFE-VYLLRDAVKGIKPEDEER 164 query 70 AAELARRTGLN 80 ::::::::::: d1im5a_ 165 ALEEMKSRGIK 175
Intermediate <-- 0.970 --> HitDALI alignment (Z-score: 5.7 Raw score:540.40) d1im5a_ 1 --pEEALIVVDmqrdfmpggalpVPEGDkIIPKVNEYIRKFKEKGALIVATRDWHpenhi 58 :::::::: ::::: :::::::::::::::::::::::::: d1rkqa_ 1 slaIKLIAIDM-------dgtllLPDHT-ISPAVKNAIAAARARGVNVVLTTGRP----- 47 d1im5a_ 59 sfrerggpwprhcvqntPGAEFV--VDLPED--AVIISK--------------------- 93 :::::: :::::: :::::: d1rkqa_ 48 ----------------yAGVHNYlkELHMEQpgDYCITYngalvqkaadgstvaqtalsy 91 d1im5a_ 94 --------------------------------------------------------ateP 97 : d1rkqa_ 92 ddyrfleklsrevgshfhaldrttlytanrdisyytvhesfvatiplvfceaekmdpntQ 151 d1im5a_ 98 DKE----------------------------------------aySGFEgtDLAKILRGN 117 ::: :::: ::::::::: d1rkqa_ 152 FLKvmmidepaildqaiaripqevkekytvlksapyfleildkrvNKGT--GVKSLADVL 209 d1im5a_ 118 GVK--RVYICgvaTEYCVRATALDAlkhgfEVYLlrdavkgikpedEERALEEMKsrgIK 175 ::: ::::: :::::::::::: :::: ::::::::: :: d1rkqa_ 210 GIKpeEIMAI--gDQENDIAMIEYA-----GVGV--------avdnAIPSVKEVA---NF 251 d1im5a_ 176 IVQ----------------f 179 ::: d1rkqa_ 252 VTKsnledgvafaiekyvln 271 FAST alignment (Normalized score: 3.30 Raw score:726.90) d1im5a_ 1 PE----EALIVVDMQRDFMPGGALPVPEGDKI-------------IPKVNEYIRKFKEKG 43 ::::: ::::::::::::::: d1rkqa_ 1 --SLAIKLIAI---------------------DMDGTLLLPDHTISPAVKNAIAAARARG 37 d1im5a_ 44 ALIVATRDWHPENHISFRERGGPWPRHCVQNTPGAE-----------FVVD-LPEDAVII 91 ::::::: :::: :::::::: d1rkqa_ 38 VNVVLTT-----------------------------GRPYAGVHNYLKELHMEQPGDYCI 68 d1im5a_ 92 SKATEPDKEAYSGFEG-------------------------------------------- 107 d1rkqa_ 69 ----------------TYNGALVQKAADGSTVAQTALSYDDYRFLEKLSREVGSHFHALD 112 d1im5a_ 108 ------------------------------------------------------------ 108 d1rkqa_ 113 RTTLYTANRDISYYTVHESFVATIPLVFCEAEKMDPNTQFLKVMMIDEPAILDQAIARIP 172 d1im5a_ 108 ---------------------------TDLAKILRGNGVK---RVYICGVATE-YCVRAT 136 :::::::::::: ::::::: :::::: d1rkqa_ 173 QEVKEKYTVLKSAPYFLEILDKRVNKGTGVKSLADVLGI-KPEEIMAIGD---QENDIAM 228 d1im5a_ 137 ALDALKHG-FEVYLLRDAVKGIKPED---EERALEEMKSRGIKIVQF------------- 179 ::: :::::: ::::::: d1rkqa_ 229 IEY-----AGVGVAV-----------DNAIPSVKEV-----------ANFVTKSNLEDGV 261 d1im5a_ 180 ---------- 180 d1rkqa_ 262 AFAIEKYVLN 271 TMalign alignment (TM-score: 0.52 Raw score:92.86) d1im5a_ 1 --PEEALIVVDM--QRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR-DWHPE 55 :::::::::: :: ::::: ::::::::::::::::::::::: :: d1rkqa_ 1 SLAIKLIAIDMDGT---LL------LPDHT-ISPAVKNAIAAARARGVNVVLTTGRP--- 47 d1im5a_ 56 NHISFRERGGPWPRHCVQNTPGAEFV--VDLP-E-DAVIISKA----------------- 94 :: ::::: :::: : :::::::: d1rkqa_ 48 -----------------YA--GVHNYLKELHMEQPGDYCITYNGALVQKAADGSTVAQTA 88 d1im5a_ 95 -----------------------T------------------------------------ 95 : d1rkqa_ 89 LSYDDYRFLEKLSREVGSHFHALDRTTLYTANRDISYYTVHESFVATIPLVFCEAEKMDP 148 d1im5a_ 96 ---EPDKE-------------------------A-Y-----S-----GFEG-TDLAKILR 115 ::::: : : : ::: :::::::: d1rkqa_ 149 NTQFLKVMMIDEPAILDQAIARIPQEVKEKYTVLKSAPYFLEILDKR-VNKGTGVKSLAD 207 d1im5a_ 116 GN-GV-K-RVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERALEEMKSR 172 :: :: : ::::: : : ::: :::::: ::::::: : :: : :::::: d1rkqa_ 208 VLGIKPEEIMAIG---D-Q--END-IAMIEY-AGVGVAV--D-------NA-I-PSVKEV 248 d1im5a_ 173 GIKIV---------Q--F----- 179 ::::: : : d1rkqa_ 249 ANFVTKSNLEDGVAFAIEKYVLN 271 HHsearch alignment (Probability: 0.03 E-value:0.05) d1im5a_ 4 ALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATRD 51 :::::::::::::: ::::::::::::::::::::::::::: d1rkqa_ 5 KLIAIDMDGTLLLP-------DHTISPAVKNAIAAARARGVNVVLTTG 45