Align 5-deoxy-glucuronate isomerase; 5DG isomerase; EC 5.3.1.30 (uncharacterized)
to candidate WP_003940746.1 C1M55_RS10195 5-deoxy-glucuronate isomerase
Query= curated2:A4IPB4 (274 letters) >NCBI__GCF_002893965.1:WP_003940746.1 Length = 290 Score = 163 bits (413), Expect = 3e-45 Identities = 109/275 (39%), Positives = 142/275 (51%), Gaps = 12/275 (4%) Query: 2 SRFIISSHSPNEEGNVVRVTPESAGWEYVGFEVYALTKGQTLRKETIDQEACLVLLKGKA 61 S++ + + S + VTPESAGW L G + ++ + E +V L G A Sbjct: 3 SKYYVPAGSSADGDFTTVVTPESAGWTESSLWTLELAPGANVHLQSGENEIIVVPLAGSA 62 Query: 62 NIHTRHERWENIGLRMDVFEKIPPYSVYVPSNDVYEVQALTDLELAVCLAPGKGTYPARL 121 + G R VF+ P YV + Y V + A+C A P R Sbjct: 63 VVVAEGTEIPLTG-RASVFDG-PSDFAYVGRDADYSVSSTGGGRFALCGARAGAKLPHRY 120 Query: 122 IPPSEVGVEMRGAGNIERRIHNILP-ESKPADSLLVVEVFTPEGNWSSYPPHKHDQHNLP 180 P S V VE+RGAGN R++HN ++ ADS++ EV TP GNWSSYP HKHD+ N Sbjct: 121 GPASGVAVELRGAGNCSRQVHNFATADTFEADSIIACEVITPGGNWSSYPSHKHDE-NSD 179 Query: 181 HESYLEETYYHQINPD----HGFMVQRVY-TDDRSIDETMVVKNGDVVLVPKGYH-PVSA 234 ES LEE YY +I+ GF RVY T +R I+ V++GDVVLVP GYH P A Sbjct: 180 VESALEEIYYFEIDRSPTGTEGFGYHRVYGTAERPIEVLEEVRSGDVVLVPHGYHGPSIA 239 Query: 235 PPGYEGYYLNVMA--GPVRTWKFRNDPDHEWVMES 267 PG+ YYLNVMA G +R W +DP H W+ S Sbjct: 240 APGHHMYYLNVMAGSGEIRAWNICDDPQHTWLRGS 274 Lambda K H 0.316 0.135 0.417 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: 294 Number of extensions: 23 Number of successful extensions: 7 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: 274 Length of database: 290 Length adjustment: 26 Effective length of query: 248 Effective length of database: 264 Effective search space: 65472 Effective search space used: 65472 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 (21.6 bits) S2: 47 (22.7 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