Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate GFF2912 PS417_14900 C4-dicarboxylate ABC transporter permease
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__WCS417:GFF2912 Length = 426 Score = 711 bits (1835), Expect = 0.0 Identities = 358/426 (84%), Positives = 399/426 (93%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 M +L LFLLLF+ MF+GVPIA+SLGLSGA++IL+FS DSV SLAIKLFETS+ YT LAIP Sbjct: 1 MAVLCLFLLLFVFMFLGVPIAISLGLSGAVSILMFSQDSVSSLAIKLFETSDAYTFLAIP 60 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 FFLLSGAFMTTGGVA+RLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS Sbjct: 61 FFLLSGAFMTTGGVAQRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180 IA+AGMVRSGYP+AFGAGI+CNAGTLGILIPPSIVMVVY+AATETSVGKLF+AGV+PGLL Sbjct: 121 IAVAGMVRSGYPKAFGAGIICNAGTLGILIPPSIVMVVYSAATETSVGKLFMAGVIPGLL 180 Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 LGL+LM+ IYIVAR+KKLPA PR + REWL SAR+A WGLLL+VIILGGIYSG FTPTEA Sbjct: 181 LGLMLMIAIYIVARIKKLPAQPRATFREWLTSARRAFWGLLLLVIILGGIYSGMFTPTEA 240 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 AAVAAVYSAFVALF+Y+DM+L +CPKVLLESG+L IMLMFIIANAMLFAHVLTTEQIPQ Sbjct: 241 AAVAAVYSAFVALFIYKDMQLRDCPKVLLESGRLAIMLMFIIANAMLFAHVLTTEQIPQE 300 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360 I +WV GL+P FL++VN+VLLIAG+FMEPSAI+LILAPIFFPIAM+LGIDPIHLGI+ Sbjct: 301 ITAWVLSEGLTPIGFLIMVNVVLLIAGSFMEPSAIVLILAPIFFPIAMKLGIDPIHLGIV 360 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420 MVVNMEIGL+ PPVGLNLFVTSAVTG+ LG TIRAALPWLMILLVFLI+VTY+P +SLAL Sbjct: 361 MVVNMEIGLVHPPVGLNLFVTSAVTGLTLGQTIRAALPWLMILLVFLIMVTYLPFISLAL 420 Query: 421 PNWLGM 426 P+WLGM Sbjct: 421 PHWLGM 426 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: 696 Number of extensions: 18 Number of successful extensions: 1 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: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 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