Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_086508323.1 BZY95_RS01930 C4-dicarboxylate ABC transporter substrate-binding protein
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_002151265.1:WP_086508323.1 Length = 319 Score = 224 bits (570), Expect = 3e-63 Identities = 126/305 (41%), Positives = 187/305 (61%), Gaps = 5/305 (1%) Query: 13 AAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKTSVQATKASVENL 71 AAA +TA +AA ++I TGGT GVYYPIG ++ N I+GA + + T ASVEN+ Sbjct: 8 AAASLMATAPLAAAQQLSIATGGTGGVYYPIGGGFAEMINNHIEGASATAEVTGASVENM 67 Query: 72 NLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAESGIKT 131 L+ G +LA +L D+V A+NG D + ++ RA+A Y N +Q+V A+S I++ Sbjct: 68 GLIMRGDADLALALADTVYQAYNGTGDFEGRQ-IENTRALASVYPNAVQLVTLADSDIQS 126 Query: 132 LDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLDATL 191 L+DL+GKR+SVGAP SGTELNARA+ +A G+ Y D R + L + E+ + I++ +DA Sbjct: 127 LEDLRGKRVSVGAPGSGTELNARALLEANGITYDDF-RPQRLNFNETADAIRDGDIDAGF 185 Query: 192 QSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIES--DAYLAGVIPAGTYDGQDADVPTVA 249 S G ++I +LA+T + V E +E + A + AG YDG D V T++ Sbjct: 186 WSVGPPTSSILNLAATRSIRLVGFSEEEIENAREVEPTFAAYELRAGMYDGMDEAVQTIS 245 Query: 250 ITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGAERF 309 I N+LV + + +E+AYQ+TKL+F+N L H AA D +E + + P+P H GA R+ Sbjct: 246 IPNVLVVNADMDEELAYQLTKLLFENTDELIAVHPAANDTTVEFSIDSTPVPFHDGALRY 305 Query: 310 YKEAG 314 Y+E G Sbjct: 306 YEEVG 310 Lambda K H 0.314 0.131 0.359 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: 265 Number of extensions: 10 Number of successful extensions: 4 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: 317 Length of database: 319 Length adjustment: 27 Effective length of query: 290 Effective length of database: 292 Effective search space: 84680 Effective search space used: 84680 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: 42 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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