Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_012709239.1 NGR_RS24810 M20 aminoacylase family protein
Query= predicted:W3Y6L2 (394 letters) >NCBI__GCF_000018545.1:WP_012709239.1 Length = 387 Score = 233 bits (595), Expect = 5e-66 Identities = 131/374 (35%), Positives = 210/374 (56%), Gaps = 9/374 (2%) Query: 12 ASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIP-FKADVYKYAVIGEIKGA 70 A++ + +V WRRH+H +PEL + T+AF++ L + G+ + + V+G I+G Sbjct: 7 AAELQNEVTEWRRHLHMNPELLFAVENTAAFVEKKLREFGVDEIVTGLGRTGVVGLIRGN 66 Query: 71 FD-GPVVGLRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQSVKDQL 129 G +GLRADMDALPITE +G ++S PG MHACGHD H A+LLGAA L ++ Sbjct: 67 LGAGRTIGLRADMDALPITETSGKAWSSTTPGKMHACGHDGHTAMLLGAAKYLAETRN-F 125 Query: 130 HGTVKLVIQPAEEEALIKGAQGIVDSGVLDD--VDEIYGLHVWPQLPVGTVGLKKGNLMA 187 G V ++ QPAEE G +V G+++ ++E+YG+H P +PVG G + G +MA Sbjct: 126 SGNVAVIFQPAEEGG--GGGNEMVKDGMMERFAIEEVYGMHNMPGMPVGHFGSRVGPIMA 183 Query: 188 ASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIGVFNSG 247 ++D F + +KG+ H A+PH ID I A + ++++ +R +P+ ++V ++ FN+G Sbjct: 184 STDEFTITVKGRGGHAAQPHKTIDPIAIGAQIVNALQTIASRTVDPLASIVVSVTKFNAG 243 Query: 248 DRYNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGHGATIND 307 +NV A L GT R P RD E R+ + +++ +G T + Y R + T+N Sbjct: 244 FAHNVIPEQAVLAGTVRALTPQVRDTGEARIRQIAESIAGAYGATVDVWYGRNYPVTVNH 303 Query: 308 ADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTGFEGNPALHNA 367 A + + T G+ V P M EDFS L GAF+++G G + LH+ Sbjct: 304 ATETGHALAVAATVAGEGNVNAALDPMMGGEDFSYMLLARPGAFVFIGNG--ESAGLHHP 361 Query: 368 AFTIDESILEPGIT 381 A+ ++ ++ GI+ Sbjct: 362 AYDFNDDVIPHGIS 375 Lambda K H 0.318 0.136 0.401 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: 398 Number of extensions: 13 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: 394 Length of database: 387 Length adjustment: 31 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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