Align agmatinase (EC 3.5.3.11) (characterized)
to candidate Echvi_3131 Echvi_3131 Arginase/agmatinase/formimionoglutamate hydrolase, arginase family
Query= BRENDA::Q8YUM9 (346 letters) >FitnessBrowser__Cola:Echvi_3131 Length = 356 Score = 344 bits (882), Expect = 2e-99 Identities = 168/344 (48%), Positives = 235/344 (68%), Gaps = 6/344 (1%) Query: 5 LQDYNPSGVGEINGNLLGLPCDYDSANLIVFAVPWEVTVSYGAGTANGPQRILDASVQLD 64 + ++P+GV G++ GLP D ++A++++ VPWEVTVSY GTANGPQ ILDAS Q+D Sbjct: 9 IDKFDPNGVSS-EGSIFGLPFDEETASVVIVPVPWEVTVSYAPGTANGPQAILDASSQVD 67 Query: 65 LFDFDHPDGWKQGIFLVEIPQEMIEKNNYYRDLAAQIIERLAQGKLLTDTPDLTPVLTEI 124 LF D D W GI ++ IP+ + N YR LA I+ L +G + V I Sbjct: 68 LFQDDITDAWTMGIHMLPIPENVYSNNTKYRILAGNYIDWLERGSPKEERERFGAVPALI 127 Query: 125 NQASQQVNQWLFTQCQAAMSQGKQVAVIGGDHSSPLGYFQALAAKYSNFGILHIDAHADL 184 ++A Q +N W++ + ++QGK VA++GGDHS+PLG+ +AL+ +YS+FGIL IDAHADL Sbjct: 128 DKACQSMNDWVYETAKDQLNQGKLVALVGGDHSTPLGHIKALSERYSSFGILQIDAHADL 187 Query: 185 RDAYEGFEFSHASIMFNGLKLPQISKLVQVGLRDISHDEVRMIEESHGRIVAYYDPMIKQ 244 RD YEGF +SHASI N L +PQ+ KLVQVG+RD +E I + RI ++D IK+ Sbjct: 188 RDQYEGFNYSHASISHNFLNIPQVEKLVQVGVRDYCEEESDRI-DGDDRITTFFDHHIKE 246 Query: 245 KLYGETNWIELSREIVNHLPEYVHISFDVDGLDPKLCPNTGTPVPGGLELEQVFCLFREL 304 +LY W + +++ LP ++I+ D+DGLDPKLCP+TGTPVPGG +L Q+ L + + Sbjct: 247 QLYEGVTWRTICDQVIASLPREIYITIDIDGLDPKLCPHTGTPVPGGFDLNQLLYLMKLI 306 Query: 305 VNSGRKIIGFDVCEVG----DAEWDGNVGARVVYKLANLMDLSH 344 V SGRKIIGFD+ EV D+EWDGNVGAR++Y+++NLM +SH Sbjct: 307 VKSGRKIIGFDLVEVAPGEDDSEWDGNVGARLLYRMSNLMGVSH 350 Lambda K H 0.320 0.139 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 395 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 346 Length of database: 356 Length adjustment: 29 Effective length of query: 317 Effective length of database: 327 Effective search space: 103659 Effective search space used: 103659 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory