Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_086508292.1 BZY95_RS01780 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_002151265.1:WP_086508292.1 Length = 444 Score = 246 bits (627), Expect = 1e-69 Identities = 160/483 (33%), Positives = 248/483 (51%), Gaps = 66/483 (13%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M +V+ ++++ L+ IG PIA ALG S L L+ G F F +AI Sbjct: 6 MGIVVAIALIV-LMAIGTPIAFALGGVSLLALMYDRGLPELIYFGETFFDRIAEFGFVAI 64 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 P FIL + + + R + R +G LPGGLA++ + AC +F+ALSGSSPAT AIG Sbjct: 65 PMFILMGAAVASSPTGRDLYRSLDLWMGRLPGGLAVSNIGACTIFSALSGSSPATCAAIG 124 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 + I MR GY AAG I GTLGILIPPS+ M++Y + E S+GR+F+AGV+PGL Sbjct: 125 KMGIPEMRTRGYPDGVAAGCIAAGGTLGILIPPSVTMIIYGISTETSIGRLFMAGVLPGL 184 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAA-------NASVG------------L 221 M + M+ + ++ G+ A AA A+V L Sbjct: 185 MLAGLFMIWTMIACRLAG-------GYANPMAQAAAQVKQNIKANVDTNLKALVRVVPFL 237 Query: 222 LLIGIILGGIYGGIFTPTEAAAVASVYAFFVATFVYR--DMGPLKSAPKPKDMGQFLTML 279 L+I IL +YGG+ TP+EAA V + +A +YR +GP+K L M Sbjct: 238 LVIAGILFALYGGVATPSEAAGVGAFLCVALAVLIYRMWQVGPIK-----------LIM- 285 Query: 280 PKMLGQTVVYFIPSFFHADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATA 339 R +L E+ V ++ VIA A + + L+ + Q +A A Sbjct: 286 --------------------RDSLRES----VMIMLVIATAEVFAYALSSMFITQTVAAA 321 Query: 340 MLSAGFGPVMFLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVN 399 + + + ++N+ LL+ G F+ P ++V+ AP++ PI + DP +I+ +N Sbjct: 322 IADMEVNRWVLMGIINLFLLVAGFFLPPVAVIVMTAPILLPIILAADFDPYWFAVILTIN 381 Query: 400 MEIGMITPPVGLNLFVTSGVA-GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNA 458 +EIG+ITPPVGLNLF+ G+A + + ++ +LP+ + + ++++ P I+ LPN Sbjct: 382 LEIGLITPPVGLNLFIIKGIAPDISLRNILLGSLPYALCMVLGIVLLCLFPGIALWLPNL 441 Query: 459 VMG 461 +MG Sbjct: 442 IMG 444 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: 659 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: 1 Length of query: 467 Length of database: 444 Length adjustment: 33 Effective length of query: 434 Effective length of database: 411 Effective search space: 178374 Effective search space used: 178374 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