Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate GFF3337 PGA1_c33900 TRAP transporter, subunit DctM
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Phaeo:GFF3337 Length = 501 Score = 175 bits (443), Expect = 4e-48 Identities = 114/432 (26%), Positives = 209/432 (48%), Gaps = 51/432 (11%) Query: 7 FSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFE--GHFTLLAIPFFI 64 F +++ L+ + VPI +++ L + L+I +D + + E + ++L +P F+ Sbjct: 11 FPVLMMLIFLRVPIGLSMFLVGLVGLIIVTDGTQVAFGRMKSETYSTFSSYSLTIVPMFL 70 Query: 65 LASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVI 124 L F T GG++ + + + +GH GG+A+A + AC F A+ GSS AT +G + + Sbjct: 71 LMGHFATLGGMSTALFKAAEGFLGHKKGGVAMAAIGACAGFGAICGSSLATAATMGRVAL 130 Query: 125 AGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMA-- 182 +R GY+ F+ + GTLGILIPPS+V+V+YA E ++ ++FLA IPG++A Sbjct: 131 PELRNYGYAGGFSTATLAAGGTLGILIPPSVVLVIYAILTEQNIAKLFLAAFIPGILAAI 190 Query: 183 GLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAA 242 G ++ ++IYV + + WGE A+ + LL+ G+++GGIY G FTPTE A Sbjct: 191 GYVIAISIYVRVFPGSAGTRPPVPWGERFAALFHVWPVLLVFGLVVGGIYLGWFTPTEGA 250 Query: 243 AVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADT-RH 301 AV + LG ++ ++ + +T Sbjct: 251 AVGA------------------------------------LGTGLIAWLNGGLNRETLTD 274 Query: 302 ALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIG 361 + + T + F++ A L +VPQ++A ++S G P M L+++ L+ Sbjct: 275 SFMVTARSTAMIFFIVLGAGFYNGFLALTKVPQELADFVVSQGLSPWMVLMLILAFYLVF 334 Query: 362 GQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMV-VNMEIGMITPPVGLNLFVTSGVA 420 G M+ ++++ P+ +P+ + ++L + ME+ P G+ Sbjct: 335 GCLMDSLSMILLTIPIFYPVISAMDFGLVNLPAMQAEAAMEVLKAGVPQGM--------- 385 Query: 421 GMPMMAVVRAAL 432 G M+A ++ A+ Sbjct: 386 GADMLASIQEAI 397 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: 616 Number of extensions: 34 Number of successful extensions: 5 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: 501 Length adjustment: 34 Effective length of query: 433 Effective length of database: 467 Effective search space: 202211 Effective search space used: 202211 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: 52 (24.6 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