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 AZOBR_RS20015 AZOBR_RS20015 C4-dicarboxylate ABC transporter
Query= TCDB::Q8YSQ7 (445 letters) >lcl|FitnessBrowser__azobra:AZOBR_RS20015 AZOBR_RS20015 C4-dicarboxylate ABC transporter Length = 503 Score = 514 bits (1323), Expect = e-150 Identities = 253/445 (56%), Positives = 338/445 (75%), Gaps = 13/445 (2%) Query: 6 EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMAN 65 E + P+MFA ++ L G+PVAF+L +LFGL+GI LG+ P A+P+R+FGIM N Sbjct: 7 ENMAPLMFAALVLFLLMGFPVAFALAANGLLFGLIGIELGLLTPALFQALPERVFGIMRN 66 Query: 66 YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125 TLLAIP+F FMG +LE+SG+AE LL+T+G L G LRGGLA AV+ VGALLAATTGVVAA Sbjct: 67 DTLLAIPFFTFMGLILERSGMAEDLLDTVGQLFGPLRGGLAYAVIFVGALLAATTGVVAA 126 Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIG 185 +V++MGLISLPIMLRYGY++ LA+GVIAASGTL QIIPPS+VL++L DQLG SVGD++ G Sbjct: 127 SVISMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIILADQLGRSVGDMYAG 186 Query: 186 SVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLV 245 +++PGL++ +A ++L+V+ +RP+ PALP + R + G L RV+ ++PPL+LI LV Sbjct: 187 ALVPGLVLTGLYAGYILVVSIVRPEFTPALPPEARSLRGFQLLFRVLTSLVPPLVLIFLV 246 Query: 246 LGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTA 305 LG+IF G ATPTE GA+G AGA+ LA Q + +RQ DTT +++S V+FILIGST Sbjct: 247 LGTIFIGIATPTEGGAMGAAGAMILALMKRQLSWSLMRQAMDTTAKLSSFVIFILIGSTV 306 Query: 306 FSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVA 365 F LVFR +NGD ++ +L +LPGG++GFL V VFLL FF+DFFE+AFI++PL PVA Sbjct: 307 FGLVFRAVNGDLWVEHLLTSLPGGELGFLIVVNIMVFLLAFFLDFFELAFIIVPLLAPVA 366 Query: 366 QKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPE-------------VTTSDI 412 +KLGIDL+W+GV+LG N+QTSF+ PPFGFALF+LR VAP E +TT I Sbjct: 367 EKLGIDLIWFGVLLGVNMQTSFMHPPFGFALFFLRSVAPREDYKDKITGKIIKKITTGQI 426 Query: 413 YRGVIPFILLQLLVLLLIIIFPGIV 437 Y G +PF+ +QL+++ L+I+FP +V Sbjct: 427 YWGAVPFVCIQLIMVALVIMFPEMV 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: 721 Number of extensions: 29 Number of successful extensions: 2 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: 503 Length adjustment: 33 Effective length of query: 412 Effective length of database: 470 Effective search space: 193640 Effective search space used: 193640 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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