Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate GFF4134 HP15_4074 C4-dicarboxylate transport system (permease large protein)
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Marino:GFF4134 Length = 423 Score = 234 bits (596), Expect = 5e-66 Identities = 142/450 (31%), Positives = 226/450 (50%), Gaps = 39/450 (8%) Query: 9 MVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHF---TLLAIPFFIL 65 ++IGLLL+G P+ V L + + ++ D GT + G +L+A+P FIL Sbjct: 4 IMIGLLLLGFPMMVPLITGAVVGFVMMFDGF--GQMGTFVQQMMGGIRPASLIAVPMFIL 61 Query: 66 ASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVIA 125 A+ MT G A R+I +A +GH+ GGLAI+ +C LF A+SGS+ ATVVA+GS + Sbjct: 62 AADIMTRGQSADRLINMVMAFIGHVKGGLAISTATSCTLFGAVSGSTQATVVAVGSPLRP 121 Query: 126 GMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAGLM 185 + + GYS F+ +I N+ + LIPPSI ++Y E S+ +F+AG+ PG+M M Sbjct: 122 KLLKAGYSDSFSLALIINSSDIAFLIPPSIGFIIYGVISETSIAELFIAGIGPGIMILFM 181 Query: 186 LMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAAVA 245 + + A V LP E WG+ A + A L II+GGIYGGIF+PTEAAAV Sbjct: 182 FSIYCLIYAHVNKLPTEEKSTWGQRAVAMREALWPLFFPVIIVGGIYGGIFSPTEAAAVC 241 Query: 246 SVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHALFE 305 +YAF + V+R S AD Sbjct: 242 VLYAFLLEFVVFR----------------------------------SLKLADIYRIAKS 267 Query: 306 AGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQFM 365 G +T + ++A +++ Q+PQ I ++ + GPV +I + V I F+ Sbjct: 268 TGLITAVVFILVAVGTGFSWIISFAQIPQAILDSVGISDMGPVGVMITICVAFFIACMFV 327 Query: 366 EPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMPMM 425 +P +++++ P+ P G+DP+ +G+++ + + IG TPP G ++F + P + Sbjct: 328 DPIVVILVLTPIFAPAIQASGLDPVLVGVLITLQVAIGSATPPFGCDIFTAIAIFKRPYL 387 Query: 426 AVVRAALPFLAVLFVFLIMITYIPWISTVL 455 V+R PF+ +L ++ P I+ L Sbjct: 388 EVIRGTPPFVFMLIAAAGLLIAFPQIALFL 417 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: 534 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 467 Length of database: 423 Length adjustment: 32 Effective length of query: 435 Effective length of database: 391 Effective search space: 170085 Effective search space used: 170085 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 17 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