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) >FitnessBrowser__azobra:AZOBR_RS20015 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:
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