Align Glutamine amidotransferase of anthranilate synthase (characterized, see rationale)
to candidate AZOBR_RS16060 AZOBR_RS16060 GMP synthase
Query= uniprot:B8DM46_DESVM (192 letters) >FitnessBrowser__azobra:AZOBR_RS16060 Length = 516 Score = 55.1 bits (131), Expect = 2e-12 Identities = 44/121 (36%), Positives = 53/121 (43%), Gaps = 5/121 (4%) Query: 74 VPVLGVCLGHQVLGLFAGATVDVGPRIMHGKTSDITHDGQGLFHG---VPSPMQVGRYHS 130 VPVLG+C G Q + G TV G+ LF G V S QV H Sbjct: 76 VPVLGICYGQQTMCHQLGGTVSGSDHREFGRAFIEVKQTCALFDGLWAVGSREQVWMSHG 135 Query: 131 LIVHAEERPDLLAVTARAPEGEVMALRYTDRPWVGVQFHPESVLTPDGVRMLANFPAHVA 190 V A PD A + A+ R + GVQFHPE V TP G ++L+NF VA Sbjct: 136 DRVTA--LPDGFQAVAVSDGAPFAAIADDARQFYGVQFHPEVVHTPHGAQLLSNFVHRVA 193 Query: 191 G 191 G Sbjct: 194 G 194 Lambda K H 0.325 0.142 0.453 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: 288 Number of extensions: 23 Number of successful extensions: 2 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: 516 Length adjustment: 27 Effective length of query: 165 Effective length of database: 489 Effective search space: 80685 Effective search space used: 80685 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 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