Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate WP_073038370.1 BUB04_RS07470 C4-dicarboxylate ABC transporter
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_900129305.1:WP_073038370.1 Length = 447 Score = 369 bits (947), Expect = e-106 Identities = 192/442 (43%), Positives = 286/442 (64%), Gaps = 6/442 (1%) Query: 6 EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMAN 65 E+L MF +V ++ G+P+A++L GVA LFGL+ G V P+ +G+M N Sbjct: 4 EFLTVAMFGTLIVAVALGHPLAYTLAGVATLFGLIDNGFNV--PMLFNMFANNCWGVMDN 61 Query: 66 YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125 Y L+AIP FIFM +L++S +AE+L E++ I+LG L+GGL LAVV+V + AATTG++ A Sbjct: 62 YVLVAIPLFIFMAQLLDRSKVAEKLFESLYIVLGSLKGGLGLAVVVVCTVFAATTGIIGA 121 Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGI---SVGDL 182 +VVAMGL++ P +L GY+K L +G+I A+GTLG +IPPS+++VV G G+ SVG+L Sbjct: 122 SVVAMGLLATPALLDKGYDKGLTSGIICAAGTLGILIPPSIMMVVYGGLTGLKETSVGNL 181 Query: 183 FIGSVIPGLMMASAFALHVLIVAFIRP-DVAPALPAQVREIGGKALGKRVIQVMIPPLIL 241 F G+VIPGL+++ + L++LI I P D P + R+ ++ ++PPL L Sbjct: 182 FAGAVIPGLILSGLYFLYILIRCTINPKDGPPISKEEARKWTAAQKWAMTLKSLVPPLAL 241 Query: 242 ILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILI 301 I +V+G+I G ATPTEA +G GA LA AN Q T + L++ TLR T+MV+ + I Sbjct: 242 IFMVMGTILGGVATPTEAAGLGALGAFILALANRQLTWQVLKEASYATLRTTAMVMMLFI 301 Query: 302 GSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLF 361 G FS VF + G + D+L + + M VF++G F+D+ I + +P+F Sbjct: 302 GGKFFSSVFLSMGGGDVVADLLIGSGLSTWAVIAIMMLIVFIMGMFVDWAAILLVTVPIF 361 Query: 362 VPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFIL 421 +P+ +L +D +W+ +++ NLQTSFLTPPFG+ALFY GVAP IYRG++PF+L Sbjct: 362 MPIVLELDVDPLWFSMLMCVNLQTSFLTPPFGYALFYFAGVAPKGYDMMVIYRGILPFVL 421 Query: 422 LQLLVLLLIIIFPGIVSFLPSL 443 LQL+ L L+ +FP +++LPSL Sbjct: 422 LQLIGLTLMALFPQTITWLPSL 443 Lambda K H 0.331 0.149 0.437 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: 531 Number of extensions: 27 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: 445 Length of database: 447 Length adjustment: 32 Effective length of query: 413 Effective length of database: 415 Effective search space: 171395 Effective search space used: 171395 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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