Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate WP_110206191.1 DNK54_RS06840 carbon-nitrogen hydrolase family protein
Query= uniprot:A0A291T0X0 (265 letters) >NCBI__GCF_003194585.1:WP_110206191.1 Length = 314 Score = 53.5 bits (127), Expect = 5e-12 Identities = 46/148 (31%), Positives = 67/148 (45%), Gaps = 4/148 (2%) Query: 4 LRTALLQNSGHPGDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIGGGVRDLAEPA 63 +R A +Q GD L + A AA++GA +V E F TG + A PA Sbjct: 8 VRVAAIQLDAALGDSDRFLADSERLATAAASEGAAWVVLPEFFTTGMGFEPRISRSAPPA 67 Query: 64 DGPSGRAVADIAAAHGLAILYGYPERHA-GAVHNSARLVGADGTELANYRKTHLYGCFER 122 +G +A +AAAHG+ I R A G V N+ L G DG L L +E Sbjct: 68 EGEPAVLLARLAAAHGIHIGGSALVRDADGHVRNAFFLFGPDG--LLGRHDKDLPTMWES 125 Query: 123 ASFTPGETPVVQATVGELTVGILVCYDV 150 A + G P G L++G+ +C+++ Sbjct: 126 ALYVGGTDPGRFDAAG-LSIGVALCWEL 152 Lambda K H 0.319 0.138 0.414 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: 216 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 265 Length of database: 314 Length adjustment: 26 Effective length of query: 239 Effective length of database: 288 Effective search space: 68832 Effective search space used: 68832 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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