Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_043917824.1 jaqu_RS04905 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_000877395.1:WP_043917824.1 Length = 476 Score = 689 bits (1778), Expect = 0.0 Identities = 363/478 (75%), Positives = 413/478 (86%), Gaps = 13/478 (2%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M+VVLLF+M+IGLLL+GVPIAV+LG SS +FLL +SD+SLAS+A + ++A GH+TLLAI Sbjct: 1 MEVVLLFTMIIGLLLVGVPIAVSLGFSSIIFLLAFSDTSLASIAQSFYQAMAGHYTLLAI 60 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFILASSFM+TGGVARRIIRFSIACVGHL GGLAIAGVFACM+FAALSGSSPATVVAIG Sbjct: 61 PFFILASSFMSTGGVARRIIRFSIACVGHLRGGLAIAGVFACMMFAALSGSSPATVVAIG 120 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 +IVIA M+Q GY+K+FAAGVICNAGTLGILIPPSIVMVVYA+A +VSVGRMFLAGV+PGL Sbjct: 121 TIVIAAMKQAGYTKDFAAGVICNAGTLGILIPPSIVMVVYASATDVSVGRMFLAGVVPGL 180 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIY------GG 234 MAGLMLM+TIYV+A++K++PKGE+ GWGEV AS +A GL+LI II+ GIY G Sbjct: 181 MAGLMLMITIYVIARIKDMPKGEFAGWGEVGASFRDAFWGLMLIVIIMIGIYGIPGVTGA 240 Query: 235 IFTPTEAAAVASVYAFFVATFVYRDMGPLKSAPKP-KDMGQFLT----MLPKMLGQTVVY 289 IFTPTEAAAVASVYAF VA F+YRD+GPL AP+P + +G + PK L Sbjct: 241 IFTPTEAAAVASVYAFIVAMFIYRDIGPL--APRPAQSVGAAVAGPVEGTPKSLFSAPWA 298 Query: 290 FIPSFFHADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVM 349 + +F H DTR LFEAGKLT+ L+F+IANALILKHVLTDEQ+PQ IA AMLSAG GP+ Sbjct: 299 LLTAFVHRDTRDTLFEAGKLTIMLMFIIANALILKHVLTDEQIPQHIAEAMLSAGLGPIT 358 Query: 350 FLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPV 409 FLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPV Sbjct: 359 FLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPV 418 Query: 410 GLNLFVTSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVMGPEIITK 467 GLNLFVTSGVAGM MMAVVRAALPFLAVLFVFLI++TYIP IS LP+A+MGPE I + Sbjct: 419 GLNLFVTSGVAGMSMMAVVRAALPFLAVLFVFLILVTYIPAISLTLPHAIMGPETIIR 476 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: 844 Number of extensions: 24 Number of successful extensions: 3 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: 476 Length adjustment: 33 Effective length of query: 434 Effective length of database: 443 Effective search space: 192262 Effective search space used: 192262 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