Align periplasmic glucoside 3-dehydrogenase (lacC subunit) (EC 1.1.99.13) (characterized)
to candidate WP_008625432.1 C943_RS06180 gluconate 2-dehydrogenase subunit 3 family protein
Query= reanno::Cola:Echvi_1848 (183 letters) >NCBI__GCF_000330725.2:WP_008625432.1 Length = 185 Score = 253 bits (646), Expect = 1e-72 Identities = 127/185 (68%), Positives = 146/185 (78%), Gaps = 2/185 (1%) Query: 1 MAMNRRDALKSFALMMGGTMVGANALLTGCTPDKQIEGLDFSPEEIDFLDEIGDTIIPTT 60 MA+NRRDA+KSF +MMGG MVGANA+LTGC P+ QI GL+FSP++I FLDEIG+ IIPTT Sbjct: 1 MAINRRDAIKSFVIMMGGAMVGANAILTGCKPEHQIIGLEFSPDDIAFLDEIGEAIIPTT 60 Query: 61 DTPGAKAVGIGSFMVMMVKDTYWEEEQKQFIDGLNSLRKGFKEEVGKDFMDASQEERTAY 120 DTPGAKA IG FMVMMVKDTY E+Q+ F DGLN + K FK GKDFM+A+ EERT+Y Sbjct: 61 DTPGAKATKIGEFMVMMVKDTYAAEQQQAFTDGLNFIIKDFKASQGKDFMEATVEERTSY 120 Query: 121 LNKLNAAAREENGPK--YFNMLKDLTVLGYFTSEIGATQALNYVEVPGKWEPCIDYKKGD 178 LN L A A G ML+DLTVLGYFTSEIGATQ L Y EVPG++EPCIDYK GD Sbjct: 121 LNGLKAKAENPEGKNAAVVKMLQDLTVLGYFTSEIGATQQLRYYEVPGRYEPCIDYKPGD 180 Query: 179 KAHAI 183 KA+AI Sbjct: 181 KAYAI 185 Lambda K H 0.316 0.135 0.395 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: 172 Number of extensions: 7 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: 183 Length of database: 185 Length adjustment: 19 Effective length of query: 164 Effective length of database: 166 Effective search space: 27224 Effective search space used: 27224 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: 44 (21.6 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