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 3609772 Dshi_3155 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Dino:3609772 Length = 429 Score = 231 bits (590), Expect = 3e-65 Identities = 141/435 (32%), Positives = 239/435 (54%), Gaps = 21/435 (4%) Query: 14 AGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIF--LTAMPQRIFGIMANYTLLAI 71 AG L LL+ PV +LF LLG G+ F F + + ++ N TL+AI Sbjct: 7 AGLLGLLALSIPVGI------VLF-LLGFGVDAFFSPFPLIRGLGNLVWSTSNNATLIAI 59 Query: 72 PYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAMG 131 P+F+ +G +L +SGIA R + + L GGL A V + +AT+G AT + Sbjct: 60 PFFVLLGEILVRSGIATRTYSALDRWVSWLPGGLVHANVATATMFSATSGSSVATAATVA 119 Query: 132 LISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPGL 191 +++P + GY+ L +G IAA GTLG +IPPS+ L+V G S+ LF+ ++PG+ Sbjct: 120 TVAMPQAEKLGYDPRLFSGAIAAGGTLGIMIPPSINLIVYGFLTQTSIPQLFLAGLVPGI 179 Query: 192 MMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIFF 251 +A F +++ IRP++ +R R + +IP ++L +++G+I+ Sbjct: 180 ALALGFMAITVVICLIRPEL-----GGLRRTFPFPEMLRALLQLIPIILLFTVIIGTIYK 234 Query: 252 GFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGST--AFSLV 309 G+ATPTEA AVG AGA+ +AA G +++ T++ITSM++ ++I ++ F+L Sbjct: 235 GWATPTEAAAVGVAGAVVIAALFGGVSVKMFADSILGTIKITSMIMLVVIAASFLNFTLA 294 Query: 310 FRGLNGD-QFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKL 368 GL + Q + D L P G + V + +LGFFI+ + + IP+ VP+ Sbjct: 295 SAGLGRELQSLLDGLGLTP---TGLILVVVLIYIVLGFFIETLSLMVVTIPIIVPLVVAQ 351 Query: 369 GIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLL 428 G D +W+G+++ ++ + +TPP G L+ ++G A S++ G IP+++ L+++ Sbjct: 352 GFDPIWFGILMIVLIEMALITPPVGLNLYVVQG-ARKSGKMSEVMVGAIPYVIAMLIMVG 410 Query: 429 LIIIFPGIVSFLPSL 443 L+I+FP I +LPS+ Sbjct: 411 LLILFPSIALYLPSV 425 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: 497 Number of extensions: 21 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: 429 Length adjustment: 32 Effective length of query: 413 Effective length of database: 397 Effective search space: 163961 Effective search space used: 163961 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 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