Align arginase (EC 3.5.3.1) (characterized)
to candidate PfGW456L13_2989 Agmatinase (EC 3.5.3.11)
Query= metacyc::MONOMER-14987 (338 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989 Length = 319 Score = 98.6 bits (244), Expect = 2e-25 Identities = 64/187 (34%), Positives = 99/187 (52%), Gaps = 13/187 (6%) Query: 151 LVLGGDHSISYPVVRAVSEKLGGPIDILHLDAHPDIYHAFEGNKYSHASSFARIMEGGYA 210 L GGDH I+YP+++A + K G + ++H DAH D + EG + H + F G Sbjct: 129 LTFGGDHFITYPLLKAHARKHGA-LSLIHFDAHSDTWPDEEGKRIDHGTMFWHAAREGLV 187 Query: 211 --RRLLQVGIRSINKEGREQGKRFGVEQYEMRTFSQD--RQFLENLKLGEGVKGVYISVD 266 R +Q+G+R+ N + + G E + R + +E ++ G VY++ D Sbjct: 188 DPSRSVQIGLRTTNDDHQ------GFEVLDARQVHRRGCEAIVEAIRARVGDNPVYLTFD 241 Query: 267 VDCMDPAFAPGVSHIEPGGLSFRDVLNILHNLQA-DVVGADVVEFNPQRDTVDGMTAMVA 325 +DC+DPAFAPG GGLS L IL L+ ++VG DVVE P D+ + +T++ A Sbjct: 242 IDCLDPAFAPGTGTPVCGGLSTVQALEILGGLRGINLVGMDVVEVAPAYDSAE-ITSLAA 300 Query: 326 AKLVREL 332 A L E+ Sbjct: 301 ATLAMEM 307 Lambda K H 0.318 0.136 0.389 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: 261 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: 338 Length of database: 319 Length adjustment: 28 Effective length of query: 310 Effective length of database: 291 Effective search space: 90210 Effective search space used: 90210 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: 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