Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate BPHYT_RS35765 BPHYT_RS35765 ABC transporter permease
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__BFirm:BPHYT_RS35765 Length = 628 Score = 205 bits (521), Expect = 4e-57 Identities = 126/418 (30%), Positives = 215/418 (51%), Gaps = 4/418 (0%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLS--GALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 ++F ++ + +F GVPI S L+ G L + F+P V + ++ E H LLA+P Sbjct: 210 VIFFVGVVAIGIFSGVPIGFSFALATFGYLGLSTFTPLEV--VVGRMDEGMSHLVLLAVP 267 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 F+ G + G+AR +I+F + VGH+ GGL+ + A L + +SGS A +AA+ Sbjct: 268 LFVFLGLLIEMTGMARAMIEFLASLVGHVHGGLSFVLIGAMYLVSGISGSKVADMAAIAP 327 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180 + M + G + ++ G IPPSIV++ + T S+ LF AG++PG + Sbjct: 328 VLFPEMKKRGASEGDLVALLATTGAQSETIPPSIVLITIGSVTGLSISALFTAGMLPGAV 387 Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 L LIL VV++ R + L R S R+ +L L L +I + G T TE Sbjct: 388 LALILCVVVWWRYRKEDLSGAQRFSKRQIGRLFVVSLPALALPFVIRMAVVEGVATATEV 447 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 + + YS + L VYR ++L+++ L+ ++FII A A LT Q Sbjct: 448 STIGIAYSMLIGLVVYRRFEWRRLGRMLVDAATLSGAILFIIGCATAMAWALTQSGFSQD 507 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360 +A + + + FL V +V ++ G+ +E I++ P+ FPIA G+ +H I+ Sbjct: 508 LAQLMGSMPGGAYGFLAVSIVVFVMLGSVLEGIPAIVLFGPLLFPIARLAGVHEVHYAIV 567 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418 ++++M +GL +PP G+ + A++ + A IR + ++ L+V LI+V IP +S+ Sbjct: 568 VILSMGVGLFSPPFGVGYYSACAISKVNPDAGIRPIVGYMGALIVGLIVVAAIPWISI 625 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: 658 Number of extensions: 35 Number of successful extensions: 2 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: 427 Length of database: 628 Length adjustment: 35 Effective length of query: 392 Effective length of database: 593 Effective search space: 232456 Effective search space used: 232456 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: 52 (24.6 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