Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_092484450.1 BM299_RS11930 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_900115975.1:WP_092484450.1 Length = 425 Score = 301 bits (772), Expect = 2e-86 Identities = 169/453 (37%), Positives = 259/453 (57%), Gaps = 35/453 (7%) Query: 4 VLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFF 63 ++LF+ L+LIGVP+A +LGLSS LL L LF + F L+AIPFF Sbjct: 3 LILFASFFVLVLIGVPVAFSLGLSSIAALLYQGQIPLIVSVQRLFTGTDS-FPLMAIPFF 61 Query: 64 ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIV 123 ++A + M TGG++RR++ F+ A VGH GGLA A MLFAA+SGS AT AIG ++ Sbjct: 62 MMAGALMNTGGISRRLVDFASAVVGHKTGGLAYVTAMASMLFAAVSGSGAATTAAIGGMM 121 Query: 124 IAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAG 183 I + + GY KEFA+ + ++G+LG++IPPSI V++ VS+ +FLAG++PG++ Sbjct: 122 IPALIKKGYGKEFASALQASSGSLGVVIPPSIPFVLFGFMSGVSIAELFLAGIVPGVLIA 181 Query: 184 LMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAA 243 ++LMV Y M K E + + E+ A LL+ IILGGI+ G FTPTEAA Sbjct: 182 VLLMVVSYFMVKNGPSTLEERVPFKEMVRRFFAALPALLMPAIILGGIFSGQFTPTEAAV 241 Query: 244 VASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHAL 303 +A VY F V FVYR++ A+ A+ Sbjct: 242 IAVVYGFIVGIFVYRELN----------------------------------LANIMEAM 267 Query: 304 FEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQ 363 +A +L ++A A ++ E +PQ+IA M S +FL++V V LLI G Sbjct: 268 KDAVISNAVVLMLLAFASTFSWIMASELIPQKIAALMSSIAPNQFIFLLLVTVFLLIIGT 327 Query: 364 FMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMP 423 F+E + L+++ P++ P+A ++ +H G++MVVN+ IGM+TPP+G+ LFV S ++ +P Sbjct: 328 FLETTPALILLVPILVPVAQTFDVNLVHFGVLMVVNLAIGMVTPPLGITLFVASNISKVP 387 Query: 424 MMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 + + RA +PF+ + L+++T++P IS +P Sbjct: 388 LANLFRAIVPFILCMIAALLVLTFVPQISLFVP 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: 596 Number of extensions: 32 Number of successful extensions: 4 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: 425 Length adjustment: 32 Effective length of query: 435 Effective length of database: 393 Effective search space: 170955 Effective search space used: 170955 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 Apr 09 2024. 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