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_004309484.1 C665_RS11110 C4-dicarboxylate ABC transporter permease
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_000310185.1:WP_004309484.1 Length = 432 Score = 223 bits (567), Expect = 1e-62 Identities = 144/436 (33%), Positives = 236/436 (54%), Gaps = 16/436 (3%) Query: 11 VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIG----LGVFDPIFLTAMPQRIFGIMANY 66 VM A L+ G +A GGV I L+ IG LG M I+ +++ Sbjct: 3 VMIAAVLI----GLMLALLAGGVWIGLALMAIGILGMLGFTPRAPGDGMAVAIWSHGSSW 58 Query: 67 TLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAAT 126 TL A+P F++MG +L ++ ++E + + + L RL G L ++ L AA +G AAT Sbjct: 59 TLTALPLFLWMGEILFRTKLSEDMFKGLSPWLERLPGRLLHTNIIGCTLFAAVSGSSAAT 118 Query: 127 VVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGS 186 +G I+LP + R GY + +A G +A +GTLG +IPPS++++V G +S+ LFIG Sbjct: 119 CATIGKIALPELQRRGYPESMALGTLAGAGTLGLLIPPSIIMIVYGVAADVSISKLFIGG 178 Query: 187 VIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVL 246 V+PG+++AS F V++ + + P PA + +G K +IP ++LI VL Sbjct: 179 VLPGILLASLFMGWVVVWSLMNPGKIPAADLKTDFMGKLRASKN----LIPVILLIGGVL 234 Query: 247 GSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAF 306 GSI+ G AT TEA A+G G++ +AA+ +S R+ M+ IL GS Sbjct: 235 GSIYSGIATATEAAAIGVIGSLIIAASQRTLNRKSFFGALMGATRLYCMIALILAGSAFL 294 Query: 307 SLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVF-LLGFFIDFFEIAFIVIPLFVPVA 365 +L + + + + + L G G L V++ + LLG F+D I + + + +P Sbjct: 295 TLAMGYIGLPRHLAEWIGGL-GLTPGMLLVALAIFYILLGCFLDGISIVVLTMAVLMPTI 353 Query: 366 QKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLL 425 Q GID +W+G+ + ++ + +TPP GF LF L+G+ ++T I R +P+ LL +L Sbjct: 354 QAAGIDPLWFGIFVVVVVEMAQVTPPVGFNLFVLQGLTGRDMTV--IARYALPYFLLMVL 411 Query: 426 VLLLIIIFPGIVSFLP 441 ++L+ FPG+V++LP Sbjct: 412 AVVLLYTFPGLVTWLP 427 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: 487 Number of extensions: 18 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: 445 Length of database: 432 Length adjustment: 32 Effective length of query: 413 Effective length of database: 400 Effective search space: 165200 Effective search space used: 165200 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