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 5208943 Shew_1444 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__PV4:5208943 Length = 465 Score = 196 bits (497), Expect = 2e-54 Identities = 144/473 (30%), Positives = 223/473 (47%), Gaps = 65/473 (13%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIF-GIMANYTLLA 70 +F + + G P+A +LG ++L LL F L ++ +++ +YTLLA Sbjct: 6 LFISLFLCMLLGMPIAIALGFSSMLTILL------FSDDSLASVALKLYESTSEHYTLLA 59 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 IP+FI A L G+A R+++ +G +RGGLA+A V+ L AA +G ATV A+ Sbjct: 60 IPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAI 119 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190 G I + M+R GY ++ A GVI SGTLG +IPPS+V++V +S +F+ +IPG Sbjct: 120 GSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPG 179 Query: 191 LMMASAFALHVLIVAFIR-------PDVAPALPAQVREIGGKALGKRVIQVMIPPLILIL 243 LMM L + IVA I+ P P + + +GG L LI+ Sbjct: 180 LMMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGG--------------LALIV 225 Query: 244 LVLGSIFFGFATPTEAGAVGCAGAIALAA--------------------------ANGQF 277 +VLGSI+ G A+PTEA AV C A +A N F Sbjct: 226 IVLGSIYGGIASPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGF 285 Query: 278 TL---------ESLRQVCDTTLRITSMVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPG 328 + + +R V +++ M++FI+ + F+ V + + + + Sbjct: 286 MVLAVFKTPADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGL 345 Query: 329 GKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKLGIDLVWYGVILGANLQTSFL 388 GFL + + G F++ I I+ P+ P+A +LGID + G+I+ N++ L Sbjct: 346 PVWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGML 405 Query: 389 TPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLLLIIIFPGIVSFLP 441 TPP G LF G+ + + IP++ L L L LI P I FLP Sbjct: 406 TPPVGLNLFVTAGITGRSM--GWVIHSCIPWLALLLFFLALITYIPQISLFLP 456 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: 440 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 465 Length adjustment: 33 Effective length of query: 412 Effective length of database: 432 Effective search space: 177984 Effective search space used: 177984 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