Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_028585565.1 G494_RS0117565 C4-dicarboxylate ABC transporter
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_000429965.1:WP_028585565.1 Length = 421 Score = 236 bits (602), Expect = 1e-66 Identities = 150/463 (32%), Positives = 247/463 (53%), Gaps = 58/463 (12%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVAL----GLSSTLFLLIYSDSSLASVAGTLFEAFEGHFT 56 + ++ L ++G L V AVAL G+ L ++I S LA Sbjct: 4 LKLLTLLLALLGSPLFIVIAAVALLSFAGVGIDLSVVIIEMSRLADTP-----------L 52 Query: 57 LLAIPFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATV 116 LLA+P FI A + ++ G +R++ S +G LPGGLA+ + C +F A +G+S T+ Sbjct: 53 LLALPLFIFAGTVLSESGTPKRLLHLSRLLLGWLPGGLAVVSLLVCAVFTAFTGASGVTI 112 Query: 117 VAIGSIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGV 176 A+G ++ + + Y + FA G+I ++G+LG+L PPS+ +++Y EV + ++FLAG+ Sbjct: 113 FALGGLLFPALIKDRYPENFALGLITSSGSLGLLFPPSLPLILYGVIAEVRIDQLFLAGI 172 Query: 177 IPG-LMAGLMLMVTIYVMAKVKNLPK---GEWLGWGEVAASAANASVGLLLIGIILGGIY 232 +PG LM L++ ++Y ++ PK GE + + A A L L I+LGGIY Sbjct: 173 LPGALMLSLLVAYSMY-----RSPPKRDPGERVSSRTIFAGLKEAGWELPLPFIVLGGIY 227 Query: 233 GGIFTPTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIP 292 GG +EAAAV ++Y V F+YRD+ L LP+++ ++++ F Sbjct: 228 GGFLVASEAAAVTALYVLVVEVFLYRDIS--------------LGQLPRLMVKSMMLF-- 271 Query: 293 SFFHADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLI 352 +L ++A ++ + L D++VP ++ + FL+ Sbjct: 272 ------------------GGILVILAASMAATNFLVDQEVPMRLFEFIRHYISSKYTFLL 313 Query: 353 VVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLN 412 ++N+ LLI G ++ L++V PL+ PIA +D IHLGII + N++IG TPPVGLN Sbjct: 314 LLNIFLLIVGSMLDIFSALILVVPLIVPIARGYEVDLIHLGIIFLTNLQIGYCTPPVGLN 373 Query: 413 LFVTSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVL 455 LF+ S P++ + A+LPFLA+L L++ITY+P +S L Sbjct: 374 LFLASYRFERPVIQLYGASLPFLALLMCTLVIITYLPLLSLFL 416 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: 536 Number of extensions: 31 Number of successful extensions: 2 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: 421 Length adjustment: 32 Effective length of query: 435 Effective length of database: 389 Effective search space: 169215 Effective search space used: 169215 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