Align TRAP dicarboxylate transporter DctP subunit; Flags: Precursor (characterized, see rationale)
to candidate Ac3H11_3226 TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
Query= uniprot:Q2IUT5 (332 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3226 Length = 339 Score = 170 bits (431), Expect = 4e-47 Identities = 106/334 (31%), Positives = 179/334 (53%), Gaps = 15/334 (4%) Query: 2 RKSIFVVASIAALALVGPAAAQ--QPIVVKFSHVVADNTPKGQAAIKFKELAEKYTNGKV 59 R+++ S+AA+ AAAQ +P +++F + + + + +G+A F E EK + GK+ Sbjct: 5 RRTLLAALSVAAITCSFQAAAQDFKPRIIRFGYGLNEVSNQGRATKLFAEEVEKASGGKM 64 Query: 60 KVEVYPNSQLFGDAKEMEAVALGDVQFIAPSLSKFDKFTKQIQVFDLPFLFNDIAAVDRF 119 KV + L D + +A+ G + + S + TK++ ++D PFLFN+ D Sbjct: 65 KVRAIGAAALGSDVQMQQALIGGAQEMMVGSTATLVGITKEMAIWDTPFLFNNAKEADVV 124 Query: 120 QAGKQGQALLRSMESKNFLGLAYWHNGMKQIS-ANRPLLKPEDAKGLKFRIQASDILAAQ 178 G GQ ++ ++ K +GL YW NG + ++ + RP+ K ED G+K R+ +++ Sbjct: 125 LDGPVGQKVMDKLQEKGLVGLVYWENGFRNLTNSKRPVNKLEDMDGIKLRVMQNNVFLDS 184 Query: 179 FQGLNATPQKLAFSEVYQALQVGTVDGQENTWSNIFSQKFYEVQKDITESDHGVIDYMVV 238 F+ L A L FSE++ AL+ TVDGQEN ++ I S KFYEVQK +T ++H ++V+ Sbjct: 185 FKTLGANAVPLPFSELFTALETKTVDGQENPYNTILSSKFYEVQKYLTVTNHVYSPWIVL 244 Query: 239 VNAKWWNGLSKD----LQDAMKKAMDEATKVNNDVAGKLNDEAKQKIASSGASKIHQLTP 294 V+ K+W+GLSK L DA KK+ D + A K + K K ++++L Sbjct: 245 VSKKYWDGLSKAEQKVLLDAAKKSRDFERQDTRAEADKALADLKGK-----GMQVNELPA 299 Query: 295 EQRKQWVEAMKPVWAKFESAIGKDL---IDAAVA 325 + + E + V A + +G+ L + AVA Sbjct: 300 AEANRMREKLSAVNASIAANVGESLWKDVQGAVA 333 Lambda K H 0.316 0.129 0.367 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: 241 Number of extensions: 9 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: 332 Length of database: 339 Length adjustment: 28 Effective length of query: 304 Effective length of database: 311 Effective search space: 94544 Effective search space used: 94544 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 (21.6 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