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 WP_083763579.1 AMB_RS21875 BAX inhibitor (BI)-1/YccA family protein
Query= TCDB::P0AAC4 (234 letters) >NCBI__GCF_000009985.1:WP_083763579.1 Length = 231 Score = 179 bits (454), Expect = 4e-50 Identities = 93/219 (42%), Positives = 140/219 (63%), Gaps = 3/219 (1%) Query: 16 GLQTYMAQVYGWMTVGLLLTAFVAWYAANSAAVMELLFTNRVFLIGLIIAQLALVIVLSA 75 GL+ YM VY +M L LT VAW A+ A+ + + + + ++A L LV + A Sbjct: 14 GLRQYMLSVYNYMASALALTGIVAWVIASVPALTAIAVYSPLKWV-FMLAPLGLVFFMGA 72 Query: 76 MIQKLSAGVTTMLFMLYSALTGLTLSSIFIVYTAASIASTFVVTAGMFGAMSLYGYTTKR 135 I + A + LF +Y+ L G +L+S+F+V+T AS+A F VTA F +SLYGYTTK+ Sbjct: 73 KIDSMRASTASTLFWVYAGLMGASLASVFLVFTGASVARVFFVTAAAFAGLSLYGYTTKK 132 Query: 136 DLSGFGNMLFMALIGIVLASLVNFWLKSEALMWAVTYIGVIVFVGLTAYDTQKLKNMGEQ 195 DLSGFG+ L M + G+++A +VN +L+S + + ++ GV++F GLTAYDTQ +K M + Sbjct: 133 DLSGFGSFLIMGVWGLMIAGIVNIFLQSPMMHFVMSAAGVLIFAGLTAYDTQNIKQMYWE 192 Query: 196 IDTRDTSNLRKYSILGALTLYLDFINLFLMLLRIFGNRR 234 D + + +K ++ GAL LY+DFINLF+ LL+ G RR Sbjct: 193 GDHSEVA--QKKAVFGALQLYMDFINLFMFLLQFMGVRR 229 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: 224 Number of extensions: 16 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: 231 Length adjustment: 23 Effective length of query: 211 Effective length of database: 208 Effective search space: 43888 Effective search space used: 43888 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