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 3608576 Dshi_1970 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Dino:3608576 Length = 688 Score = 370 bits (951), Expect = e-107 Identities = 199/464 (42%), Positives = 294/464 (63%), Gaps = 29/464 (6%) Query: 6 EWLGPVMFAGALVLLSSGYPVAFSLGGVAILF---------------GLLGIGLGVFDPI 50 E L MF + LL +GYPVA+ L GV + + GL G G+ D + Sbjct: 226 EKLVVAMFITFIALLFTGYPVAWVLSGVGVAYCGLAFLFDNDLMLWTGLEGTLTGL-DYL 284 Query: 51 FLTAMPQRIFGIMANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVV 110 L A R++ M+N L+A+P FIFMG ML++SG+AERL+ +M L G+ RGGLA+ V Sbjct: 285 TLGATVNRVYATMSNAVLVALPMFIFMGLMLDESGVAERLMTSMQRLFGKTRGGLAITVT 344 Query: 111 LVGALLAATTGVVAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVV 170 ++G +LAA+TG++ A+VV +G++SLP M++ Y+ LA GV++ASGTLG +IPPS++LV+ Sbjct: 345 MIGIILAASTGIIGASVVLLGVLSLPAMMQQKYSPRLAAGVVSASGTLGILIPPSIMLVI 404 Query: 171 LGDQLGISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKR 230 + DQ+ +SVGDLF+ +V PG+++ + +++ ++++++PDVAP +P + +A+ K Sbjct: 405 MADQMALSVGDLFMAAVFPGVIIGGLYLVYIFVISYLKPDVAP-VPEGAQSPDWQAV-KD 462 Query: 231 VIQVMIPPLILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTL 290 V+ ++P L LIL VLGSIF G TPTEA +G GA LA + TL L V +T Sbjct: 463 VMVAVLPTLGLILAVLGSIFAGICTPTEASGIGALGATLLALGYRKLTLHKLVNVLVSTF 522 Query: 291 RITSMVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDF 350 T+ + I +G+T FS V R L GD + ++A G G + + VFLLGF +D+ Sbjct: 523 NTTAYIFAIFLGATVFSYVLRELGGDALIEHMIAATGLGPNGTILFILFIVFLLGFVLDW 582 Query: 351 FEIAFIVIPLFVPVAQKLGID-----------LVWYGVILGANLQTSFLTPPFGFALFYL 399 EI IV+PL P+ LG+D LVW+ +++ LQTSFLTPP GFALFYL Sbjct: 583 IEITLIVLPLMRPIVNALGMDIPGFGVLDEPTLVWFVILVAVTLQTSFLTPPVGFALFYL 642 Query: 400 RGVAPPEVTTSDIYRGVIPFILLQLLVLLLIIIFPGIVSFLPSL 443 +GV PPE+ DIY+G+IPF+LLQL L L+ + P + ++LPS+ Sbjct: 643 KGVCPPEIKLLDIYKGIIPFVLLQLTGLALVFLLPALATWLPSV 686 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: 818 Number of extensions: 35 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: 688 Length adjustment: 36 Effective length of query: 409 Effective length of database: 652 Effective search space: 266668 Effective search space used: 266668 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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