Align The YbhL (AceP) protein. Possibly a pmf-dependent acetate uptake transporter. [14C]Acetate uptake was inhibited by CCCP as well as cold acetate, serine, α-ketoglutarate, lactate, and succinate (M. Inouye, personal communication) (characterized)
to candidate 3610288 Dshi_3668 protein of unknown function UPF0005 (RefSeq)
Query= TCDB::P0AAC4 (234 letters) >FitnessBrowser__Dino:3610288 Length = 244 Score = 174 bits (442), Expect = 1e-48 Identities = 104/228 (45%), Positives = 146/228 (64%), Gaps = 5/228 (2%) Query: 11 VQPRAGLQTYMAQVYGWMTVGLLLTAFVAWYAANSAAVMELLFTNRVFLIGLIIAQLALV 70 +Q GL+ Y+ V+ +M GL+L+A VA+ AN A V L+F + + I A LALV Sbjct: 16 LQYDVGLRKYLTGVFAYMGGGLVLSALVAFAVANVAPVTALIFGTPLKWVA-IFAPLALV 74 Query: 71 IVLSAMIQKLSAGVTTMLFMLYSALTGLTLSSIFIVYTAASIASTFVVTAGMFGAMSLYG 130 + S ++LS G LF ++AL G++L+S +V+T SI F+ + +F M+L+G Sbjct: 75 MFASFRFERLSVGALQGLFWGFAALMGVSLASALLVFTGTSIVQAFLSASIIFLTMALWG 134 Query: 131 YTTKRDLSGFGNMLFMALIGIVLASLVNFWLKSEALMWAVTYIGVIVFVGLTAYDTQKLK 190 YTTKRDLSG+G+ L + LIG++ AS+VN +L S AL AV+ IGVIVF GLTA D Q+L+ Sbjct: 135 YTTKRDLSGWGSFLMIGLIGVIGASIVNLFLASGALAMAVSVIGVIVFTGLTASDMQRLR 194 Query: 191 N----MGEQIDTRDTSNLRKYSILGALTLYLDFINLFLMLLRIFGNRR 234 N EQ +NL K I+GAL+LYL+ INLF MLL +FG R+ Sbjct: 195 NEYLAHCEQGGVATQANLGKLQIMGALSLYLNLINLFQMLLSLFGQRQ 242 Lambda K H 0.330 0.140 0.403 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: 189 Number of extensions: 11 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: 234 Length of database: 244 Length adjustment: 23 Effective length of query: 211 Effective length of database: 221 Effective search space: 46631 Effective search space used: 46631 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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