Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate AO356_25640 AO356_25640 L-dehydroascorbate transporter large permease subunit
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25640 Length = 426 Score = 240 bits (612), Expect = 8e-68 Identities = 142/462 (30%), Positives = 243/462 (52%), Gaps = 42/462 (9%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M +V+ +IG + +G+PIA AL L ++ L++Y D A + F L+A+ Sbjct: 1 MTLVIFLGSLIGSMALGMPIAFAL-LVVSVALMVYLDLFDAQIIAQNLLNGADSFPLMAV 59 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFF+LA M GG+++RI+ ++A VGH GGL + A L A+LSGS+ A A+ Sbjct: 60 PFFMLAGEIMNVGGLSKRIVNIAMALVGHKRGGLGYVAIIASCLLASLSGSAVADAAALA 119 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 ++++ M G+++ +AG+I + +IPPSI +V+ A VS+ ++FLAG++PGL Sbjct: 120 ALLVPMMVLAGHNRGRSAGLIAAGSIIAPVIPPSIGFIVFGVASGVSISKLFLAGIVPGL 179 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240 M G L V + +++ +N+ EV + + S + L II+ G+ GIFTPTE Sbjct: 180 MLGASLAVAWWYISRSENVETPPKRSRAEVLRTLLDGSWAMGLPLIIILGLKFGIFTPTE 239 Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300 AA VA+VY+ FV+ +YR+M + Sbjct: 240 AAVVAAVYSLFVSLVIYREMKV----------------------------------SQLY 265 Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360 + + K T ++ ++A A++ ++T +P Q+A + + L+V+ V++++ Sbjct: 266 EVILSSAKTTSVVMLLVAAAMVSSWLVTIADLPGQLAELLAPFMDNQTVLLLVMMVLIIL 325 Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420 G M+ + ++I+ P++ P I+ GIDP++ G++ ++N IG+ITPPVG L V GVA Sbjct: 326 VGTVMDMTPTILILTPVLMPAVIQAGIDPVYFGVLFLINTAIGLITPPVGTVLNVVCGVA 385 Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVMGP 462 + +VR PF+ FV L ++ + P V+GP Sbjct: 386 KLDFEEIVRGVWPFMFAQFVVLFLL-------VLFPQLVLGP 420 Lambda K H 0.329 0.144 0.421 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: 577 Number of extensions: 39 Number of successful extensions: 5 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: 467 Length of database: 426 Length adjustment: 32 Effective length of query: 435 Effective length of database: 394 Effective search space: 171390 Effective search space used: 171390 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 (21.8 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