Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_012706777.1 NGR_RS12335 M20 aminoacylase family protein
Query= predicted:W3Y6L2 (394 letters) >NCBI__GCF_000018545.1:WP_012706777.1 Length = 389 Score = 251 bits (640), Expect = 3e-71 Identities = 142/377 (37%), Positives = 212/377 (56%), Gaps = 6/377 (1%) Query: 18 QVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYKYAVIGEIKGAFDGPVVG 77 ++VA RR +H+HPEL EE+ TSAFI L LG + K V+G +K +G Sbjct: 13 ELVAIRRDLHAHPELGLEERRTSAFIAGHLEALGYTVTTGLAKTGVVGTLKVGAGPRSIG 72 Query: 78 LRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQSVKDQLHGTVKLVI 137 +RAD+DALPI E TGL + S+ PG+MHACGHD H A+LLGAA L ++ GT+ L+ Sbjct: 73 IRADIDALPILEETGLDYASKTPGLMHACGHDGHTAMLLGAARALAERRN-FDGTIHLIF 131 Query: 138 QPAEEEALIKGAQGIVDSGVLDDV--DEIYGLHVWPQLPVGTVGLKKGNLMAASDRFLVH 195 QPAEE GA+ ++D G+ D D ++ LH P LP G L++G + AA D + Sbjct: 132 QPAEEN--FGGAKIMIDEGLFDKFPCDAVFALHNEPNLPFGQFALREGPIGAAVDEARIT 189 Query: 196 IKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIGVFNSGDRYNVGSG 255 + G+ HGAEP D IV A+ ++ ++++V+R +PMD V T+G F++G N+ Sbjct: 190 VHGRGGHGAEPQETADPIVCGASIVMALQTIVSRNIHPMDPTVVTVGAFHAGSASNIIPE 249 Query: 256 DAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGHGATINDADAIDYVT 315 A + R++DPA RD +ERR+ +A FG +T++Y+R + ATIN D+V Sbjct: 250 RAEIVVGIRSFDPAVRDALERRIRMIAEAQAASFGMRATVDYQRSYDATINHKSETDFVR 309 Query: 316 HIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTGFEG-NPALHNAAFTIDES 374 + + G D VV P M +EDF+ L + G + +LG+ G LH+ + ++ Sbjct: 310 DLAVRFAGADKVVDLARPYMGSEDFAYMLKERPGTYFFLGSRVTGEEKPLHHPGYNFNDD 369 Query: 375 ILEPGITMMAGIAAELL 391 +L G +A L Sbjct: 370 LLPIGAAFWTELAEAYL 386 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: 425 Number of extensions: 18 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: 389 Length adjustment: 31 Effective length of query: 363 Effective length of database: 358 Effective search space: 129954 Effective search space used: 129954 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