Align periplasmic glucoside 3-dehydrogenase (lacC subunit) (EC 1.1.99.13) (characterized)
to candidate WP_008626954.1 C943_RS09210 gluconate 2-dehydrogenase subunit 3 family protein
Query= reanno::Cola:Echvi_1848 (183 letters) >NCBI__GCF_000330725.2:WP_008626954.1 Length = 197 Score = 85.5 bits (210), Expect = 5e-22 Identities = 58/192 (30%), Positives = 95/192 (49%), Gaps = 28/192 (14%) Query: 3 MNRRDALKSFALMMGGTMVGANA---LLTGCTPDKQIEGLD--FSPEEIDFLDEIGDTII 57 MNRRDA++ ALM GT G + LL C+ +++ + S ++ F+ DTI+ Sbjct: 1 MNRRDAIRKTALM-AGTAAGVPSFLSLLQACSKQERLTWVPEFLSEDQARFISAFVDTIL 59 Query: 58 PTTDTPGAKAVGIGSFMVMMVKDTYWEEEQKQFIDGLNSLRKGFKEEVGKDFMDASQEER 117 P TDTPGA V F+ ++ TY ++ Q+ + + K++ G F D S E++ Sbjct: 60 PKTDTPGALDVKADVFIDLVYARTYDQKAQENVVAEIEKFNATAKDKFGNVFADLSLEDK 119 Query: 118 TAYLNKLNAAAREENGPK-----------------YFNMLKDLTVLGYFTSEIGATQALN 160 TA+L + +E N PK ++ LK +T+ YF+SE L+ Sbjct: 120 TAFLKE-----QEANSPKFNPRVWGTAVGKQEPVGFYRGLKSMTLWAYFSSEEIGKNVLS 174 Query: 161 YVEVPGKWEPCI 172 Y +PG+++ CI Sbjct: 175 YDPIPGEYKGCI 186 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: 101 Number of extensions: 9 Number of successful extensions: 3 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: 197 Length adjustment: 20 Effective length of query: 163 Effective length of database: 177 Effective search space: 28851 Effective search space used: 28851 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