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 GFF2912 PS417_14900 C4-dicarboxylate ABC transporter permease
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__WCS417:GFF2912 Length = 426 Score = 206 bits (524), Expect = 1e-57 Identities = 144/434 (33%), Positives = 225/434 (51%), Gaps = 22/434 (5%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLAI 71 +F V + G P+A SLG L G + I + F ++++ ++F YT LAI Sbjct: 6 LFLLLFVFMFLGVPIAISLG----LSGAVSILM--FSQDSVSSLAIKLFETSDAYTFLAI 59 Query: 72 PYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAMG 131 P+F+ GA + G+A+RL++ +G +RGGLA+A VL L AA +G ATV A+G Sbjct: 60 PFFLLSGAFMTTGGVAQRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119 Query: 132 LISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPGL 191 I++ M+R GY K G+I +GTLG +IPPS+V+VV SVG LF+ VIPGL Sbjct: 120 SIAVAGMVRSGYPKAFGAGIICNAGTLGILIPPSIVMVVYSAATETSVGKLFMAGVIPGL 179 Query: 192 MMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIFF 251 ++ + + IVA I+ LPAQ R + L + L+L++++LG I+ Sbjct: 180 LLGLMLMIAIYIVARIK-----KLPAQPRATFREWLTS--ARRAFWGLLLLVIILGGIYS 232 Query: 252 GFATPTEAGAVGCA-GAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSLVF 310 G TPTEA AV A L +V + R+ M++FI+ + F+ V Sbjct: 233 GMFTPTEAAAVAAVYSAFVALFIYKDMQLRDCPKVLLESGRLAIMLMFIIANAMLFAHV- 291 Query: 311 RGLNGDQFMFDVLA-NLPGG--KIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQK 367 L +Q ++ A L G IGFL + + + G F++ I I+ P+F P+A K Sbjct: 292 --LTTEQIPQEITAWVLSEGLTPIGFLIMVNVVLLIAGSFMEPSAIVLILAPIFFPIAMK 349 Query: 368 LGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVL 427 LGID + G+++ N++ + PP G LF V +T R +P++++ L+ L Sbjct: 350 LGIDPIHLGIVMVVNMEIGLVHPPVGLNLFVTSAVT--GLTLGQTIRAALPWLMILLVFL 407 Query: 428 LLIIIFPGIVSFLP 441 +++ P I LP Sbjct: 408 IMVTYLPFISLALP 421 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: 432 Number of extensions: 19 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: 426 Length adjustment: 32 Effective length of query: 413 Effective length of database: 394 Effective search space: 162722 Effective search space used: 162722 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