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 CA265_RS23435 CA265_RS23435 hypothetical protein
Query= TCDB::P0AAC4 (234 letters) >FitnessBrowser__Pedo557:CA265_RS23435 Length = 251 Score = 167 bits (423), Expect = 2e-46 Identities = 93/237 (39%), Positives = 142/237 (59%), Gaps = 13/237 (5%) Query: 11 VQPRAGLQTYMAQVYGWMTVGLLLTAFVAWYAANSAAVMELLFTNR---------VFLIG 61 VQ ++ + + V+ WM V L ++ A++ A++ AV++ L + V Sbjct: 15 VQEKSASKRFFGNVFLWMFVALAVSTVAAYFIASTPAVLDYLLSYNPQTGKGGFTVLGYI 74 Query: 62 LIIAQLALVIVLSAMIQKLSAGVTTMLFMLYSALTGLTLSSIFIVYTAASIASTFVVTAG 121 I A L LV ++ A +Q++S +F+LYS LTG+ LS I + Y+ S+ +F A Sbjct: 75 AIFAPLGLVFLMGAGMQRMSYQALIGVFLLYSILTGVMLSFILLTYSLPSVVISFAAAAA 134 Query: 122 MFGAMSLYGYTTKRDLSGFGNMLFMALIGIVLASLVNFWLKSEALMWAVTYIGVIVFVGL 181 +F M++ GYTT DLS FG +LF +IG+V+ S++N +L S L + + +IGV +F L Sbjct: 135 IFAVMAIMGYTTDTDLSKFGPILFAGVIGLVIISIINMFLGSSTLGYIMGFIGVAIFTAL 194 Query: 182 TAYDTQKLKNMGEQID----TRDTSNLRKYSILGALTLYLDFINLFLMLLRIFGNRR 234 TAY Q+LK +GE +D T + +K +I+GAL+LY+ FINLFL LLRIFGNRR Sbjct: 195 TAYKVQELKRIGEGLDENGNTLGVNESKKLAIMGALSLYITFINLFLSLLRIFGNRR 251 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: 197 Number of extensions: 8 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: 234 Length of database: 251 Length adjustment: 23 Effective length of query: 211 Effective length of database: 228 Effective search space: 48108 Effective search space used: 48108 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