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_011842536.1 RSPH17029_RS18465 TRAP transporter large permease subunit
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_000015985.1:WP_011842536.1 Length = 453 Score = 388 bits (997), Expect = e-112 Identities = 204/444 (45%), Positives = 294/444 (66%), Gaps = 15/444 (3%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGV--------FD-PIFLTAMPQRIFGI 62 +F ++LL +G+PVA+ LGG ++++ ++G+ L V FD L +P+RI+G Sbjct: 11 LFGTFVLLLMTGFPVAWVLGGTSVIWTVIGV-LSVEQFGADLWFDYDSSLALLPERIWGN 69 Query: 63 MANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGV 122 + + L+A+P F FMG ML++SGIAERL+ M L GR+RGG A+ V+++G LLAATTG+ Sbjct: 70 VESQALVALPMFTFMGIMLDQSGIAERLMHDMVRLFGRVRGGYAVTVIIIGVLLAATTGI 129 Query: 123 VAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGI---SV 179 + A+VV +G++SLP M+ Y++ A G A+GTLG +IPPS++LV++ D+L SV Sbjct: 130 IGASVVLLGMLSLPTMMENNYSRSFAAGTACATGTLGILIPPSIMLVMMADRLATPEASV 189 Query: 180 GDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPL 239 G LF+G+ IPGLM+ + + +I +P +AP PA I + + V+ + +P Sbjct: 190 GALFMGAFIPGLMLGLLYIAYAIIRPLFQPSIAPT-PANPERITLRLVFDTVLAI-VPTA 247 Query: 240 ILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFI 299 +LIL VLGSIF G ATPTEA VG GA+ LAA N + TL LR+ T R T+ + I Sbjct: 248 VLILSVLGSIFMGIATPTEASGVGAFGALLLAALNRRLTLPVLRRSLYATTRTTAFIFGI 307 Query: 300 LIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIP 359 +G+TAFS+V RGL GD+ + L LP G G + + VF+LGFF+D+ EI IV+P Sbjct: 308 FLGATAFSVVLRGLGGDEVIEAALLGLPFGPNGIVIAILFAVFILGFFLDWIEITLIVLP 367 Query: 360 LFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPF 419 L P Q+LG DLVW+ ++ LQTSFLTPP GFALFY++GVAPPE+T DIY+GV+P+ Sbjct: 368 LVAPAVQQLGFDLVWFTILFAICLQTSFLTPPVGFALFYIKGVAPPEITVLDIYKGVVPY 427 Query: 420 ILLQLLVLLLIIIFPGIVSFLPSL 443 IL+QL L L+ FP + +LP++ Sbjct: 428 ILIQLFALALVFAFPALAVWLPAM 451 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: 614 Number of extensions: 32 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: 453 Length adjustment: 33 Effective length of query: 412 Effective length of database: 420 Effective search space: 173040 Effective search space used: 173040 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