Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_049989147.1 LT39_RS03805 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_000784335.1:WP_049989147.1 Length = 431 Score = 241 bits (616), Expect = 3e-68 Identities = 144/463 (31%), Positives = 240/463 (51%), Gaps = 39/463 (8%) Query: 1 MDVVLLFSMVIGLL---LIGVPIAVALGLSSTLFLLIYSDS-SLASVAGTLFEAFEGHFT 56 MDVVL+ ++ LL LIGVP+A ALGL+S + +L S S VA TL + F Sbjct: 1 MDVVLIALFILVLLALYLIGVPVAFALGLTSLILMLTPMVSYSPELVAQTLVSGADS-FV 59 Query: 57 LLAIPFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATV 116 LLAIP F+L +M + G+ I F+ +G + GG+A + A +LF+ ++G++ A Sbjct: 60 LLAIPLFLLTGLYMNSFGLTSIIFDFAEEMIGPIRGGIAHVNILASILFSGMTGTAAADA 119 Query: 117 VAIGSIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGV 176 +G+I M+ GY K ++A V ++ +G +IPPS+ +++Y +VS+G +F+AG+ Sbjct: 120 AGLGAIEYEAMQDAGYEKGYSAAVTGSSAIIGPIIPPSVPLIMYGILAQVSIGVLFIAGI 179 Query: 177 IPGLMAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIF 236 +PGL+ G L++ A +G W ++ S A+ L +I+GG+ GG F Sbjct: 180 VPGLIMGATLLMLCTYYAHSHGYERGTWWSLPDIWESFKTAAPALGTPVLIIGGLLGGFF 239 Query: 237 TPTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFH 296 T TEA AVA Y FV Y + + G F+ Sbjct: 240 TATEAGAVALFYTLFVGYVFYGGV----------ENGDFV-------------------- 269 Query: 297 ADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNV 356 +E T L F++A+A + ++ Q+P +A A++ P + L+++ Sbjct: 270 ----ETTYEGVVTTAALTFIVASATLYGFLVRRAQLPDALAEAVIGVTGDPTLLLLMIVG 325 Query: 357 ILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVT 416 +LLI G ME + I+ P+ P+ GIDPIH GI+M++ + IG++TPP G+ LF+ Sbjct: 326 VLLIVGLMMETIAAITILTPVFLPVIDVAGIDPIHFGIVMILTLMIGLLTPPFGIILFIL 385 Query: 417 SGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAV 459 V + + ++R+ +PF L + L+++ +P ++ LP V Sbjct: 386 EKVTDVGLERIMRSMVPFYIPLLIILLLVVVLPGLTLWLPKFV 428 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: 618 Number of extensions: 28 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: 467 Length of database: 431 Length adjustment: 33 Effective length of query: 434 Effective length of database: 398 Effective search space: 172732 Effective search space used: 172732 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 24 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