Align N-succinylglutamate synthase (characterized)
to candidate 353287 BT3761 hypothetical protein (NCBI ptt file)
Query= reanno::Btheta:353287 (192 letters) >FitnessBrowser__Btheta:353287 Length = 192 Score = 393 bits (1009), Expect = e-114 Identities = 192/192 (100%), Positives = 192/192 (100%) Query: 1 MDTQQIDVMVADASHEVYVDTILETIRNAAAVRGTGIAERTHEYVATKMKEGKAIIALCG 60 MDTQQIDVMVADASHEVYVDTILETIRNAAAVRGTGIAERTHEYVATKMKEGKAIIALCG Sbjct: 1 MDTQQIDVMVADASHEVYVDTILETIRNAAAVRGTGIAERTHEYVATKMKEGKAIIALCG 60 Query: 61 DTFAGFTYIESWGNKQYVATSGLIVHPDFRGLGLAKRIKQASFQLARLRWPKAKIFSLTS 120 DTFAGFTYIESWGNKQYVATSGLIVHPDFRGLGLAKRIKQASFQLARLRWPKAKIFSLTS Sbjct: 61 DTFAGFTYIESWGNKQYVATSGLIVHPDFRGLGLAKRIKQASFQLARLRWPKAKIFSLTS 120 Query: 121 GAAVMKMNTELGYVPVTFNELTDDEAFWKGCEGCTNHDILAAKNRKFCICTAMLYDPTDP 180 GAAVMKMNTELGYVPVTFNELTDDEAFWKGCEGCTNHDILAAKNRKFCICTAMLYDPTDP Sbjct: 121 GAAVMKMNTELGYVPVTFNELTDDEAFWKGCEGCTNHDILAAKNRKFCICTAMLYDPTDP 180 Query: 181 RNIKKEQERNNI 192 RNIKKEQERNNI Sbjct: 181 RNIKKEQERNNI 192 Lambda K H 0.320 0.134 0.404 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: 242 Number of extensions: 3 Number of successful extensions: 1 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: 192 Length of database: 192 Length adjustment: 20 Effective length of query: 172 Effective length of database: 172 Effective search space: 29584 Effective search space used: 29584 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 (21.9 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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