Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate 3610805 Dshi_4191 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__Dino:3610805 Length = 331 Score = 156 bits (395), Expect = 6e-43 Identities = 102/315 (32%), Positives = 169/315 (53%), Gaps = 9/315 (2%) Query: 10 ATGLA-AAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKG 68 A GLA AA+L ASAQD +R + ++ + + F + + G + ++ Sbjct: 9 ALGLATAALLVAGTASAQDTLE--LRMSVESTPGASTQQILAAFRDALQAEMGDAVAIEY 66 Query: 69 FADASLGSDI-QMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDG 127 F +LG +I MQ G + +GS A V + FAVFD+PFLFN+ + AV DG Sbjct: 67 FDSGTLGDEIVHMQQVRTGQLDVIPIGSDA--VQLDPKFAVFDIPFLFNSRDQVAAVLDG 124 Query: 128 PFGQKLAAKLNDK-GLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFN 186 P G +L + GL L + E GFR++TN+ RPV DL+G+KLR + I F Sbjct: 125 PIGAELDQSFQENAGLKVLGFGEIGFRHITNNVRPVVTPADLEGLKLRTPGSSTRIMSFE 184 Query: 187 GFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLAS 246 GA+ + ++ E++ A++ G +DGQENP I + EVQKY+++S+HVY+P ++ + Sbjct: 185 MLGASPIKMNIGEVYLALQQGVIDGQENPFGNIAKWSWDEVQKYISLSRHVYTPITLVMN 244 Query: 247 KRWYDGLSADERKIINEAAVASRDFERKDSRE--ASKQSIAYLKDKGMQINELSDAELGR 304 R Y+GL+ ++R ++ AA + D R E AS +++ + +++NE+ A Sbjct: 245 LRTYEGLTDEQRDAVHAAARVAVDSSRAYGAENDASLEAVIRERSPDVELNEIDAASFRD 304 Query: 305 MREMVKPAMDKFAAD 319 + + + + K A + Sbjct: 305 VAKAIGAEIGKTAGE 319 Lambda K H 0.317 0.134 0.372 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: 222 Number of extensions: 11 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: 337 Length of database: 331 Length adjustment: 28 Effective length of query: 309 Effective length of database: 303 Effective search space: 93627 Effective search space used: 93627 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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