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 3610014 Dshi_3395 TRAP C4-dicarboxylate transport system permease DctM subunit (RefSeq)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Dino:3610014 Length = 482 Score = 360 bits (925), Expect = e-104 Identities = 197/463 (42%), Positives = 297/463 (64%), Gaps = 36/463 (7%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGL-----LGIGLGVFDPIF-----------LTAM 55 MF + LL G PVA++L GV+++F L L F I L + Sbjct: 21 MFLVFIYLLFRGIPVAYALVGVSLIFALVAEIFLDPNRAAFRDIIEFDRTGIDYQRLQVL 80 Query: 56 PQRIFG-IMANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGA 114 R+FG I+ N L+A+P FIFMG ML++SG+A+R++ +M L G LRGGL+L V+L+G Sbjct: 81 SGRLFGNIVKNPVLVALPMFIFMGLMLDQSGVAQRMMHSMQKLFGGLRGGLSLTVMLIGI 140 Query: 115 LLAATTGVVAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQ 174 +LAA+TGV+ A+V +G+++LP M++ Y+K +ATG IA++GTLG +IPPS++LV++ DQ Sbjct: 141 ILAASTGVIGASVTLLGVMALPAMMQQNYSKPIATGTIASAGTLGILIPPSIMLVIMSDQ 200 Query: 175 LGISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQV 234 L IS+GDLF+G++ PGL++ + + + ++ I P PA P Q E+G + K V+ Sbjct: 201 LAISLGDLFMGALFPGLILGALYIIFIIAYGLINPKAMPA-PPQTDEVGWDVV-KDVLLA 258 Query: 235 MIPPLILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITS 294 ++PP+ LILLVLGSIF GFATPTEA +G GA LA ANG+ + L++V +TL + Sbjct: 259 VVPPMFLILLVLGSIFAGFATPTEASGLGALGATLLALANGRLNFKVLKEVSRSTLNTSG 318 Query: 295 MVVFILIGSTAFSLVFRGLNGDQFMFD-VLANLPGGKIGFLFVSMTTVFLLGFFIDFFEI 353 +V I + + F+LV R GD+ + VL+ + LF+ + +FLLGF +D+ EI Sbjct: 319 YIVGIFLAANFFALVLRRYGGDEIIQGYVLSTFSDPYMIVLFI-LFIIFLLGFLLDWIEI 377 Query: 354 AFIVIPLFVPVAQKLGIDL-------------VWYGVILGANLQTSFLTPPFGFALFYLR 400 I++PL +P+ +G+DL VW+ +++ LQTSFLTPP GFALFYL+ Sbjct: 378 TIIIMPLMLPII--VGLDLAVPGFDQVRDPAVVWFAILVAVTLQTSFLTPPVGFALFYLK 435 Query: 401 GVAPPEVTTSDIYRGVIPFILLQLLVLLLIIIFPGIVSFLPSL 443 GV PP V+ IY+G+IPF++LQLL L ++ FP + ++LP++ Sbjct: 436 GVCPPGVSLGHIYKGIIPFVMLQLLGLFIVFQFPALTTWLPAI 478 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: 676 Number of extensions: 34 Number of successful extensions: 5 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: 482 Length adjustment: 33 Effective length of query: 412 Effective length of database: 449 Effective search space: 184988 Effective search space used: 184988 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