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_011842505.1 RSPH17029_RS18290 TRAP transporter large permease subunit
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_000015985.1:WP_011842505.1 Length = 438 Score = 336 bits (862), Expect = 8e-97 Identities = 176/440 (40%), Positives = 279/440 (63%), Gaps = 11/440 (2%) Query: 3 LAYEWLGP---VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRI 59 LA +GP +MF +VLL SG P+AF VA++F L+G G P+ + + RI Sbjct: 7 LAALGIGPSTLIMFGTMVVLLLSGMPLAFVTLLVALIFALVGFG-----PMAVGLITSRI 61 Query: 60 FGIMANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAAT 119 + + N+ +++P F+ M AML++SG+A L + M ++ GR+RGG+A+ + V +LAA Sbjct: 62 YTFVNNFIFVSVPMFVLMAAMLDRSGVARDLFDAMKLIGGRIRGGVAVQTIFVSVILAAM 121 Query: 120 TGVVAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISV 179 +G++ +V +GL++LP MLR GY+K LA GV+ A G+LG +IPPS+VL++ G +S+ Sbjct: 122 SGIIGGEIVLLGLLALPQMLRLGYDKNLAIGVVCAGGSLGAMIPPSIVLIMYGLTANVSI 181 Query: 180 GDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPL 239 G LF + IPG M+A + +VLI+++ +P VAP P V I A R+++ +I P+ Sbjct: 182 GSLFSAAFIPGAMLAGFYVAYVLIMSYFKPGVAP--PPVVETIP-TAEKLRLLKGLILPI 238 Query: 240 ILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFI 299 ++++ VLGSI+ G A+ TEA AVG G A G+F+ LR TL M+V+I Sbjct: 239 MVVVFVLGSIYGGIASVTEASAVGVGGVALSALLRGEFSWAFLRDSAMQTLATVGMIVWI 298 Query: 300 LIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIP 359 IG+TA V+ + G F+ ++ + + + M +F+LG F+D+ IA + +P Sbjct: 299 GIGATALVGVYNLMGGISFVSGLITGVSDNPTVIILLMMAILFVLGAFLDWVGIALLTMP 358 Query: 360 LFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPF 419 +FVP+ + LG+D VW+GV+ N+Q SFL+PPFG A FYL+ VAPP+++ DI++ ++PF Sbjct: 359 IFVPIVKSLGLDPVWFGVLFCMNMQVSFLSPPFGPAAFYLKSVAPPDISLGDIFKALLPF 418 Query: 420 ILLQLLVLLLIIIFPGIVSF 439 I LQ+L L ++I+FPGI + Sbjct: 419 IGLQILALAVMILFPGIAIY 438 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: 587 Number of extensions: 37 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: 438 Length adjustment: 32 Effective length of query: 413 Effective length of database: 406 Effective search space: 167678 Effective search space used: 167678 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 Apr 10 2024. 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