Align L-lactate dehydrogenase complex protein LldG (characterized, see rationale)
to candidate Echvi_1567 Echvi_1567 Uncharacterized conserved protein
Query= uniprot:Q8EGS6 (189 letters) >FitnessBrowser__Cola:Echvi_1567 Length = 195 Score = 142 bits (357), Expect = 5e-39 Identities = 80/191 (41%), Positives = 118/191 (61%), Gaps = 2/191 (1%) Query: 1 MSSKHEILNALKLSALTNHPMPSIDVAPRVEDLVGQFETNLKTVAGTLHREGGLAALQAK 60 M+SK IL A+K + +P + P + L+ ++E L G L LA ++A Sbjct: 1 MTSKESILAAIKNNKPEASSLPDLLSFPEEDHLIERYEKGLTGNGGKLKVVDTLAEVEAF 60 Query: 61 VDELIAQGLQVISLVEGVTANRDVPPTA--HELRDIDYAVIPGDVGVAENGAIWVNNKNL 118 V E + + SLV+ V N DV + H+L ++ A++ G +GV+ENGAIW+ KN+ Sbjct: 61 VKENYSNDQLIASLVDEVKGNVDVHKISDPHDLEHVELAILKGALGVSENGAIWMPEKNI 120 Query: 119 GHRVTPFICENLILALPIHKIVPNMHQAAKEVTLDAGEFGVFIAGPSKTADIEQALVVGA 178 HRV PFI ++LI+ + ++ NMHQA ++V + A +GVFIAGPSKTADIEQ+LV+GA Sbjct: 121 VHRVLPFIAQHLIIVIHEETLLTNMHQAYEKVQVAADGYGVFIAGPSKTADIEQSLVIGA 180 Query: 179 HGACSLNVYLV 189 HG SL V+L+ Sbjct: 181 HGPRSLTVFLL 191 Lambda K H 0.318 0.135 0.390 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: 107 Number of extensions: 5 Number of successful extensions: 1 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: 189 Length of database: 195 Length adjustment: 20 Effective length of query: 169 Effective length of database: 175 Effective search space: 29575 Effective search space used: 29575 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 (21.7 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Sep 17 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