Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate AO356_25640 AO356_25640 L-dehydroascorbate transporter large permease subunit
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25640 Length = 426 Score = 278 bits (712), Expect = 2e-79 Identities = 146/418 (34%), Positives = 247/418 (59%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 MT++ L M +G+PIA +L + ++ + +A L ++ + L+A+P Sbjct: 1 MTLVIFLGSLIGSMALGMPIAFALLVVSVALMVYLDLFDAQIIAQNLLNGADSFPLMAVP 60 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 FF+L+G M GG+++R+++ A A VGH RGGL A++A L A+LSGS+ A AA+ + Sbjct: 61 FFMLAGEIMNVGGLSKRIVNIAMALVGHKRGGLGYVAIIASCLLASLSGSAVADAAALAA 120 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180 + + MV +G+ + AG++ + +IPPSI +V+ A+ S+ KLF+AG+VPGL+ Sbjct: 121 LLVPMMVLAGHNRGRSAGLIAAGSIIAPVIPPSIGFIVFGVASGVSISKLFLAGIVPGLM 180 Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 LG L V + ++R + + P+ S E L + W + L +II+ G+ G FTPTEA Sbjct: 181 LGASLAVAWWYISRSENVETPPKRSRAEVLRTLLDGSWAMGLPLIIILGLKFGIFTPTEA 240 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 A VAAVYS FV+L +YR+M++S+ +V+L S K T ++M ++A AM+ + ++T +P Sbjct: 241 AVVAAVYSLFVSLVIYREMKVSQLYEVILSSAKTTSVVMLLVAAAMVSSWLVTIADLPGQ 300 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360 +A + + + LLV+ +++++ G M+ + ILIL P+ P ++ GIDP++ G++ Sbjct: 301 LAELLAPFMDNQTVLLLVMMVLIILVGTVMDMTPTILILTPVLMPAVIQAGIDPVYFGVL 360 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418 ++N IGLITPPVG L V V + +R P++ V L ++ P + L Sbjct: 361 FLINTAIGLITPPVGTVLNVVCGVAKLDFEEIVRGVWPFMFAQFVVLFLLVLFPQLVL 418 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: 458 Number of extensions: 29 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