Align phosphoribosylanthranilate isomerase subunit (EC 5.3.1.24) (characterized)
to candidate WP_012741188.1 EUBREC_RS01195 phosphoribosylanthranilate isomerase
Query= metacyc::MONOMER-301 (205 letters) >NCBI__GCF_000020605.1:WP_012741188.1 Length = 221 Score = 110 bits (276), Expect = 1e-29 Identities = 77/184 (41%), Positives = 105/184 (57%), Gaps = 7/184 (3%) Query: 3 RVKICGITNLEDALFSVESGADAVGFV-FYPKSKRYISPEDARRISVELPPFVFRVGVFV 61 ++KICG+T+ +A + E+ D G V F+PKSKR IS E A+ I L + RV V V Sbjct: 22 KIKICGLTSPAEARYLNENHVDFAGMVLFFPKSKRNISIEQAKDIMAALDASIKRVAVVV 81 Query: 62 NEEPEKILDVASYVQLNAVQLHGEEPIELCRKIAERILVIKAVGVSNERDMERALN-YRE 120 + E+I + + + VQ+HGE P E + A I ++KA VS+ E+ N R Sbjct: 82 SPSIEQIRQIEA-AGFDYVQIHGEIP-ETEAEAAIAIPILKAFNVSDMDSYEKYHNDSRI 139 Query: 121 FPILLDTKTPEYGGSGKTFDWSLILPYRDRFRYLVLSGGLNPENVRSAIDVVRPFAVDVS 180 + D P GSGKTFDW L+ + L+L+GGLNP+NVR AI+ V P VDVS Sbjct: 140 AGYVFDAIEP---GSGKTFDWKLVDNIPRDEKLLLLAGGLNPDNVRMAIEAVHPDGVDVS 196 Query: 181 SGVE 184 SGVE Sbjct: 197 SGVE 200 Lambda K H 0.321 0.140 0.408 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: 123 Number of extensions: 7 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: 205 Length of database: 221 Length adjustment: 22 Effective length of query: 183 Effective length of database: 199 Effective search space: 36417 Effective search space used: 36417 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 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Apr 13 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