Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_086509695.1 BZY95_RS09470 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_002151265.1:WP_086509695.1 Length = 419 Score = 300 bits (769), Expect = 5e-86 Identities = 166/445 (37%), Positives = 254/445 (57%), Gaps = 36/445 (8%) Query: 5 LLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFFI 64 LLF + +L+GVPIA+A+G +STL L L V +F+ F L+A+P FI Sbjct: 4 LLFLLFFAFMLLGVPIALAIG-ASTLLALNAQGVPLMVVTQQMFQGINS-FALVAVPMFI 61 Query: 65 LASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVI 124 LA M G V+ +++ F+ + G L GGL++ V A M FAA+SGS AT A+GS ++ Sbjct: 62 LAGDLMAQGKVSEKLVDFADSLFGFLKGGLSLVSVGAGMFFAAISGSGAATTAAVGSSLV 121 Query: 125 AGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAGL 184 +++ GY AA +I +GT+G++IPPS+ M++YA + SV ++FL G++PG++ G+ Sbjct: 122 PELKRKGYDPASAASLIAASGTIGVVIPPSVPMIIYAVVAQQSVSKLFLNGIVPGILMGI 181 Query: 185 MLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAAV 244 L A +N P+G L + + +AS GL+ IILGGI+ GIFTP+EAA V Sbjct: 182 GLAAIAITQAYRRNYPRGTALSLATIWRTFKSASWGLMTPVIILGGIFSGIFTPSEAAVV 241 Query: 245 ASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHALF 304 A YA V+ FVYRD+ LG D L Sbjct: 242 AVNYALLVSLFVYRDLS---------------------LG-------------DVYRILI 267 Query: 305 EAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQF 364 + T ++ VIA + +L L+ QVP IA +LS P + ++++ ++L+ G F Sbjct: 268 RSAITTAVIMLVIATSAVLSWTLSSWQVPGTIAQTVLSLSTNPYVIMLLIVAVILLTGVF 327 Query: 365 MEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMPM 424 +E + L+I+ P++ P+ ++LGIDPIH GII+V+ + IGMITPPV +NL+V S V +P+ Sbjct: 328 IETASALIILTPVLLPLVLQLGIDPIHFGIIIVMGLAIGMITPPVAINLYVASSVTQLPL 387 Query: 425 MAVVRAALPFLAVLFVFLIMITYIP 449 + RA LP+L L L+++ Y+P Sbjct: 388 ERITRAILPYLLGLIGVLLLVVYVP 412 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: 554 Number of extensions: 40 Number of successful extensions: 5 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: 467 Length of database: 419 Length adjustment: 32 Effective length of query: 435 Effective length of database: 387 Effective search space: 168345 Effective search space used: 168345 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