Align Acetate permease A; Monocarboxylate transporter acpA (characterized)
to candidate 5208392 Shew_0904 GPR1/FUN34/yaaH family protein (RefSeq)
Query= SwissProt::Q5B2K4 (298 letters) >FitnessBrowser__PV4:5208392 Length = 188 Score = 87.8 bits (216), Expect = 2e-22 Identities = 67/198 (33%), Positives = 97/198 (48%), Gaps = 19/198 (9%) Query: 81 KFANPAPLGLSAFALTTFVLSCINMGARDITHPNIVIALAFGYGGLVQLLAGMWEMAVGN 140 K ANPAPLGL F +TT +L+ N G I +++A+ YGGL Q+L GM G+ Sbjct: 4 KLANPAPLGLMGFGMTTVLLNIHNAGFFAIDA--MILAMGIFYGGLGQVLVGMMCFKRGD 61 Query: 141 TFGATALSSYGGFWIAF-AIVLTPGGFNIQTALTAENGDEAMFYNSFGLFLMGWFIFTTI 199 TFG TA +SYG FW+ +++ P + L A + M G +L W +FT Sbjct: 62 TFGTTAFTSYGLFWLTLVGLIMLP-----KLGLAAASPSHFM-----GWYLSLWGLFTAF 111 Query: 200 MLFCTLRSTVAFFLLFLFLDLAFLLLGVGYIQRDDAGQPNPPVIKAGGFFGLLAAFAAWY 259 M +LR A ++F L + F LL RD G +I GF G+ +A Y Sbjct: 112 MFVGSLRYPRAKQVVFGSLTILFFLLAA----RDFTGSELIGMI--AGFEGIFCGASAIY 165 Query: 260 NALAGIADSSNSFFIIPV 277 A+A + + I+P+ Sbjct: 166 FAMAQVLNQEYGRVILPI 183 Lambda K H 0.324 0.139 0.436 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: 164 Number of extensions: 11 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: 298 Length of database: 188 Length adjustment: 23 Effective length of query: 275 Effective length of database: 165 Effective search space: 45375 Effective search space used: 45375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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