Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_043919376.1 jaqu_RS12740 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_000877395.1:WP_043919376.1 Length = 457 Score = 240 bits (612), Expect = 8e-68 Identities = 154/468 (32%), Positives = 246/468 (52%), Gaps = 35/468 (7%) Query: 3 VVLLFSMVIGLL-LIGVPIAVALG--LSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLA 59 +V + S+ + +L ++GVP+ + +G + F+L L ++ L + F F LLA Sbjct: 6 IVTMISIGVTILFMLGVPVFLVIGWWVVGMSFVL---GLPLLNIGAALSDVFTDGFALLA 62 Query: 60 IPFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAI 119 +P FIL + G+ARR+ F+ +C+G + GGLA+A + AC LFAA+SGS+ AT I Sbjct: 63 MPLFILTGDLINRSGIARRLSDFAYSCLGWIRGGLAMASIGACGLFAAISGSNSATTATI 122 Query: 120 GSIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPG 179 GS++ M + GY + F+A GTLGI+IPPSI+ +VY + + + +F+AG++PG Sbjct: 123 GSMLHPEMTKGGYDERFSAATAAAGGTLGIIIPPSIIFIVYGFLLNLPISDLFVAGILPG 182 Query: 180 -LMAGLMLMVTIYVMAKVKNLPKGEWLGWG--------EVAASAANASVGLLLIGIILGG 230 LMAG M+ V + GWG V + A +G IG++L G Sbjct: 183 ILMAGAMMTACFIVCWR---------NGWGILIGLSPARVIKTGIGAWLGFFAIGLVLWG 233 Query: 231 IYGGIFTPTEAAAVA---SVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTV 287 IY G F+PTEAA V + F+ +Y+ M + KP+D +ML Sbjct: 234 IYTGKFSPTEAAGVTVGFCIIVGFLCLPLYKLM-HRRDGEKPEDRAIEERGFAEML---- 288 Query: 288 VYFIPSFFHADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGP 347 + F + + ++T L +IA +++++ +L+ + I+ + S G G Sbjct: 289 --LVQGFGPTELPSITMRSAQITGILAPLIAVSVVMQQILSVLGAQEAISAFVTSMG-GY 345 Query: 348 VMFLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITP 407 L I+ + G +E + +I+AP++ PIA +G+DPI +I +V IG ITP Sbjct: 346 HAVLFTAMAIVFVSGMVLESLPVTIILAPILAPIAAGVGVDPIQFAVIFLVGASIGFITP 405 Query: 408 PVGLNLFVTSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVL 455 P GLNL+V SGV G+P ++R LP+L L + I +P +ST L Sbjct: 406 PYGLNLYVASGVTGVPYFRLLRYILPYLVALILAWFTIALVPGLSTAL 453 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: 618 Number of extensions: 30 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: 457 Length adjustment: 33 Effective length of query: 434 Effective length of database: 424 Effective search space: 184016 Effective search space used: 184016 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