Align arginase (EC 3.5.3.1) (characterized)
to candidate BPHYT_RS26640 BPHYT_RS26640 agmatinase
Query= metacyc::MONOMER-14987 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS26640 Length = 300 Score = 103 bits (258), Expect = 4e-27 Identities = 84/271 (30%), Positives = 131/271 (48%), Gaps = 14/271 (5%) Query: 65 GVPLGHNSSFLQGPAFAPPRIREAMWCGSTNSTTEEGKELDDPRILTDVGDVPVQELRDA 124 G+PL ++F G F P +R A + G + D + D GD Sbjct: 26 GIPLDLATTFRPGTRFGPAGVRAASVQLAELGAFPWGVDPFDHLNVVDYGDCWFDAHNPL 85 Query: 125 GVDDDRLMSIISESVKLVMEENPLRPLVLGGDHSISYPVVRAVSEKLGGPIDILHLDAHP 184 G+ D +II+ + ++ + R L GGDH I+YP++ A EK G P+ ++H DAH Sbjct: 86 GIRD----AIIAHARGILA--SGARMLTFGGDHYITYPLLVAHVEKYGKPLSLIHFDAHC 139 Query: 185 DIYHAFEGNKYSHASSFARIMEGGYA--RRLLQVGIRSINKEGREQGKRFGVEQYEMRTF 242 D + + +H + F + + R +Q+GIR+ N + G R + R Sbjct: 140 DTWPDDNPDSLNHGTMFYKAIRERLVDPARSVQIGIRTWNDD--FMGVRILDAPWVHRNG 197 Query: 243 SQDRQFLENLKLGEGVKGVYISVDVDCMDPAFAPGVSHIEPGGLSFRDVLNILHNLQA-D 301 +Q ++ + G Y++ D+DC+DPAFAPG GGLS L I+ L A + Sbjct: 198 TQ--AAIDEVLSIVGNAPAYLTFDIDCLDPAFAPGTGTPVAGGLSSAQALEIVRALGAVN 255 Query: 302 VVGADVVEFNPQRDTVDGMTAMVAAKLVREL 332 +VGADVVE +P D D +TA+ AA L ++ Sbjct: 256 LVGADVVEVSPPYDHSD-VTALAAAHLASDM 285 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: 283 Number of extensions: 15 Number of successful extensions: 4 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: 300 Length adjustment: 27 Effective length of query: 311 Effective length of database: 273 Effective search space: 84903 Effective search space used: 84903 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: 48 (23.1 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