Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate AZOBR_RS09605 AZOBR_RS09605 C4-dicarboxylate ABC transporter
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__azobra:AZOBR_RS09605 Length = 336 Score = 181 bits (458), Expect = 3e-50 Identities = 103/328 (31%), Positives = 188/328 (57%), Gaps = 5/328 (1%) Query: 6 SVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLK 65 S+L AT A ++A AA+AQ+ P +I+F + ++ + +G+ + F + +R+ GK+K Sbjct: 5 SLLCATVAAGCLMAATAATAQE--PIVIKFSHVVAPETPKGKGAEKFKQLAEQRTAGKVK 62 Query: 66 VKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGI-VKDFAVFDLPFLFNNEQEADAV 124 V+ + ++ L D + AL GA +M+ S A + K+F +FDLP++F + V Sbjct: 63 VEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGAKEFEIFDLPYIFPCKTALVKV 122 Query: 125 FDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDM 184 GP G++L KL +KG+ GL YW+NGF+ + ++ +P+ D KG+K+R+ + V Sbjct: 123 TTGPIGKQLFQKLENKGITGLAYWDNGFK-IMSANKPLHATADFKGLKMRIQSSKVLDAQ 181 Query: 185 FNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVL 244 GA ++FSE++ A++TG VDG ENP + + + K +EVQ + T+S H Y + V+ Sbjct: 182 MRALGALPQVMAFSEVYQALQTGVVDGTENPPSNMYTQKMHEVQSHATLSDHGYLGYAVI 241 Query: 245 ASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKG-MQINELSDAELG 303 +K+++DGL AD R ++ A + ++ ++E + +++ +K G + EL+ E Sbjct: 242 VNKKFWDGLPADVRTQLDGAMKEATEYANNIAQEENDKALEAMKAAGKTKFYELTKDERA 301 Query: 304 RMREMVKPAMDKFAADGGADLLNELQGE 331 R+ + P + A+ G +LL ++ E Sbjct: 302 SWRQAMLPVHEDMASRVGKELLASIKTE 329 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: 225 Number of extensions: 7 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: 1 Length of query: 337 Length of database: 336 Length adjustment: 28 Effective length of query: 309 Effective length of database: 308 Effective search space: 95172 Effective search space used: 95172 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