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 GFF3856 HP15_3797 TRAP-type mannitol/chloroaromatic compound transport system, large permease component
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Marino:GFF3856 Length = 454 Score = 392 bits (1008), Expect = e-114 Identities = 204/443 (46%), Positives = 298/443 (67%), Gaps = 13/443 (2%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGLLGI------GLGV-FD-PIFLTAMPQRIFGIM 63 MF LL +GYPVA+ LGG A+++ ++G+ G + FD + +P+RI+ ++ Sbjct: 11 MFLTFGALLMTGYPVAWVLGGTAVIWTVVGVVAVENFGANLWFDYQSSMGLVPERIWKVV 70 Query: 64 ANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVV 123 ++ TL+A+P FIFMG ML++SG+AERL+ +M L G +RGG A+ V+++G LLAATTG++ Sbjct: 71 SSETLVALPMFIFMGIMLDQSGVAERLMNSMVKLFGAVRGGYAVTVIVIGVLLAATTGII 130 Query: 124 AATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGI---SVG 180 A+VV +G++SLP+M+ Y+K A G A+GTLG +IPPS++LV++ D+L + SVG Sbjct: 131 GASVVLLGMLSLPVMMENKYDKGFAVGTACATGTLGILIPPSIMLVLMADRLAVPEASVG 190 Query: 181 DLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLI 240 DLF+G+ PGLM+ + + + +I ++P++AP +P ++ A+ V + ++P Sbjct: 191 DLFMGAFFPGLMLGAMYVAYAIIRPMLQPNIAP-VPEGTEKVSW-AIVWEVAKAVVPTAA 248 Query: 241 LILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFIL 300 LIL VLGSIF G ATPTEA VG GA+ LA +G+ L L T R + + I Sbjct: 249 LILGVLGSIFAGIATPTEASGVGALGALLLALMSGRLNLNVLNSSMQQTTRTAAFIFAIF 308 Query: 301 IGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPL 360 +G+TAFS+V RGL GDQ + D L LP G G + + VFLLGFF+D+ EI I++PL Sbjct: 309 LGATAFSVVLRGLGGDQVIEDALLGLPFGPYGVVLTILFGVFLLGFFLDWVEITLIILPL 368 Query: 361 FVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFI 420 PV Q LG DLVW+ ++ LQTSFLTPP GFALFY++GVAPPE+ +DIYRGVIPFI Sbjct: 369 VAPVVQSLGFDLVWFTILFAMCLQTSFLTPPVGFALFYIKGVAPPEIKVTDIYRGVIPFI 428 Query: 421 LLQLLVLLLIIIFPGIVSFLPSL 443 ++QL L ++ + P I ++LPS+ Sbjct: 429 IIQLAALAIVFVVPEIATWLPSV 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: 616 Number of extensions: 24 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: 454 Length adjustment: 33 Effective length of query: 412 Effective length of database: 421 Effective search space: 173452 Effective search space used: 173452 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