Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate GFF3337 PGA1_c33900 TRAP transporter, subunit DctM
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Phaeo:GFF3337 Length = 501 Score = 213 bits (543), Expect = 8e-60 Identities = 122/353 (34%), Positives = 199/353 (56%), Gaps = 8/353 (2%) Query: 7 FLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRS---LAIKLFETSEHYTLLAIPFFL 63 F +L +L+F+ VPI +S+ L G + +++ + + + + + + T Y+L +P FL Sbjct: 11 FPVLMMLIFLRVPIGLSMFLVGLVGLIIVTDGTQVAFGRMKSETYSTFSSYSLTIVPMFL 70 Query: 64 LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123 L G F T GG++ L A +GH +GG+A+AA+ AC F A+ GSS AT A +G +A+ Sbjct: 71 LMGHFATLGGMSTALFKAAEGFLGHKKGGVAMAAIGACAGFGAICGSSLATAATMGRVAL 130 Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL--L 181 + GY F + GTLGILIPPS+V+V+YA TE ++ KLF+A +PG+L + Sbjct: 131 PELRNYGYAGGFSTATLAAGGTLGILIPPSVVLVIYAILTEQNIAKLFLAAFIPGILAAI 190 Query: 182 GLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAA 241 G ++ + IY+ P V E A+ LL+ +++GGIY G FTPTE A Sbjct: 191 GYVIAISIYVRVFPGSAGTRPPVPWGERFAALFHVWPVLLVFGLVVGGIYLGWFTPTEGA 250 Query: 242 AVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSI 301 AV A+ + +A ++ + + + + T M+ FI+ A + L ++PQ + Sbjct: 251 AVGALGTGLIA-WLNGGLNRETLTDSFMVTARSTAMIFFIVLGAGFYNGFLALTKVPQEL 309 Query: 302 ASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPI--AMELGI 352 A +V GLSPWM L+++ L+ G M+ ++IL+ PIF+P+ AM+ G+ Sbjct: 310 ADFVVSQGLSPWMVLMLILAFYLVFGCLMDSLSMILLTIPIFYPVISAMDFGL 362 Lambda K H 0.330 0.144 0.425 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: 519 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 427 Length of database: 501 Length adjustment: 33 Effective length of query: 394 Effective length of database: 468 Effective search space: 184392 Effective search space used: 184392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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