Align L-lactate dehydrogenase complex protein LldG (characterized, see rationale)
to candidate 353983 BT4457 conserved hypothetical protein (NCBI ptt file)
Query= uniprot:Q8EGS6 (189 letters) >FitnessBrowser__Btheta:353983 Length = 193 Score = 107 bits (268), Expect = 1e-28 Identities = 69/193 (35%), Positives = 108/193 (55%), Gaps = 6/193 (3%) Query: 1 MSSKHEILNALKLSALTNHPMPSIDVAPRVE--DLVGQFETNLKTVAGTLHREGGLAALQ 58 MSS+ EIL +++ T + P I R+ D + QF + V GT+ G + Sbjct: 1 MSSREEILASIRKHTQTRYEKPDIADMKRLTYPDKIEQFCAISRAVGGTVVVLGEGEDVN 60 Query: 59 AKVDELIAQGLQVISLVEGV---TANRDVPPTAHELRDIDYAVIPGDVGVAENGAIWVNN 115 A + +++ S++ + T N D+ EL + AVI G++GVAENGA+W+ Sbjct: 61 AVIRRTYPDAMRIASVLPDISCATFNPDMVDDPKELDGTEVAVIRGEIGVAENGAVWIP- 119 Query: 116 KNLGHRVTPFICENLILALPIHKIVPNMHQAAKEVTLDAGEFGVFIAGPSKTADIEQALV 175 + + ++ FI E L++ + +KIV M+ A +++ +FG FI+GPSKTADIEQALV Sbjct: 120 QTVKYKAIYFISEKLVILIDRNKIVDTMYDAYRKLDGQEYQFGTFISGPSKTADIEQALV 179 Query: 176 VGAHGACSLNVYL 188 +GAHGA + V L Sbjct: 180 MGAHGAREVLVIL 192 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: 88 Number of extensions: 5 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: 189 Length of database: 193 Length adjustment: 20 Effective length of query: 169 Effective length of database: 173 Effective search space: 29237 Effective search space used: 29237 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