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 | d1rcua_ | Hypothetical protein TM1055 | Putative lysine decarboxylase | Putative lysine decarboxylase | 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 <-- 0.996 --> HitDALI alignment (Z-score: 7.6 Raw score:619.00) d1im5a_ 1 PEEALIVVDmQRDFMPggalpvPEGDKIIPKVNEYIRKFKEKGALIVATRDwhpenhisf 60 ::::::::: :::::: ::::::::::::::::::::::::::::: d1rcua_ 1 MKKVVVVGY-SGPVNK------SPVSELRDICLELGRTLAKKGYLVFNGGR--------- 44 d1im5a_ 61 rerggpwprhcvqntpgaefVVDLP------eDAVIISKATE-------pdkeaysgFEG 107 ::::: :::::::::: ::: d1rcua_ 45 ----------------dgvmELVSQgvreaggTVVGILPDEEagnpylsvavktgldFQM 88 d1im5a_ 108 T--DLAKILrgngvKRVYICGVAteYCVRATALDALKHGFEVYLLRDAVKgikpedeeRA 165 : :::::: ::::::::: ::::::::::::::::::::::::: :: d1rcua_ 89 RsfVLLRNA-----DVVVSIGGE--IGTAIEILGAYALGKPVILLRGTGG-----wtdRI 136 d1im5a_ 166 LEE---mKSRG------IKIVQF----------- 179 ::: :::: :::::: d1rcua_ 137 SQVlidgKYLDnrriveIHQAWTveeavqiieqi 170 FAST alignment (Normalized score: 5.81 Raw score:1013.00) d1im5a_ 1 -PEEALIVVDMQRDFMPGGALPVP---------EGDKIIPKVNEYIRKFKEKGALIVATR 50 :::::: :::::::::::::::::::::::::: d1rcua_ 1 MKKVVVV-----------------GYSGPVNKSPVSELRDICLELGRTLAKKGYLVFNG- 42 d1im5a_ 51 DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLP-----------------EDAVIISK 93 :::::::: d1rcua_ 43 -----------------------------------GRDGVMELVSQGVREAGGTVVGILP 67 d1im5a_ 94 ATEPDKEAYSGFEG-----------------------TDLAKILRGNGVKRVYICGVATE 130 ::::: ::::::::: :: d1rcua_ 68 --------------DEEAGNPYLSVAVKTGLDFQMRSFVLLR-----NADVVVSIG--GE 106 d1im5a_ 131 YCVRATALDALKHGFEVYLLRDAVKGIKPED----EERALEEMKS-------------RG 173 :::::::::::::::::::::: :::::: :: d1rcua_ 107 IGTAIEILGAYALGKPVILLRG---------TGGWTDRISQ----VLIDGKYLDNRRIVE 153 d1im5a_ 174 IKIVQF------------ 179 ::::: d1rcua_ 154 IHQAW-TVEEAVQIIEQI 170 TMalign alignment (TM-score: 0.57 Raw score:101.34) d1im5a_ 1 PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATRDWHPENHISF 60 :::::::::::: ::: ::::::::::::::::::::::::::::: d1rcua_ 1 MKKVVVVGYSGP-VNK------SPVSELRDICLELGRTLAKKGYLVFNGGR--------- 44 d1im5a_ 61 RERGGPWPRHCVQNTPG-AEFVV-D-LP---EDAVIISKATE-------------PDKEA 101 : : :::: : :: :::::::: :: :::: d1rcua_ 45 ----------D-----GV-MELVSQGVREAGGTVVGILP-DEEAGNPYLSVAVKT-GLDF 86 d1im5a_ 102 YSGFEGTDLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPED 161 ::::: :::: :: : ::::: :: ::::::::::::::::::::::: ::: : d1rcua_ 87 QMRSF-VLLR-NA----D-VVVSI-GG-EIGTAIEILGAYALGKPVILLRG-TGG----W 132 d1im5a_ 162 EERALEEM---KSR------GIKIVQ---F-------- 179 :::::::: ::: :::::: : d1rcua_ 133 TDRISQVLIDGKYLDNRRIVEIHQAWTVEEAVQIIEQI 170 HHsearch alignment (Probability: 0.02 E-value:0.24) d1im5a_ 130 EYCVRATALDALKHGFEVYLLR 151 :::::::::::::::::::::: d1rcua_ 106 EIGTAIEILGAYALGKPVILLR 127