Align TRAP dicarboxylate transporter DctP subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_051305824.1 G494_RS0117445 TRAP transporter substrate-binding protein
Query= uniprot:Q2IUT5 (332 letters) >NCBI__GCF_000429965.1:WP_051305824.1 Length = 325 Score = 132 bits (332), Expect = 1e-35 Identities = 82/263 (31%), Positives = 135/263 (51%), Gaps = 7/263 (2%) Query: 3 KSIFVVASIAALALVGPA--AAQQPIVVKFSHVVADNTPKGQAAIKFKELAEKYTNGKVK 60 K + + S+ + L G AAQ+ +K V + + AA KFK+L E+ + G+ Sbjct: 2 KHLQLTLSLVLVLLFGQLSLAAQE---IKLGVVTKPGSAQNIAAEKFKQLLEQASEGRYT 58 Query: 61 VEVYPNSQLFGDAKEMEAVALGDVQFIAPSLSKFDKFTKQIQVFDLPFLFNDIAAVDRFQ 120 V +Y + L + + ++ + +G VQ ++ FD F ++V + PFLF D D Sbjct: 59 VRIYHSKALGNETEILQQIQMGTVQLGIITVGPFDTFAPIVRVINYPFLFKDNQQADAIL 118 Query: 121 AGKQGQALLRSMESKNFLGLAYWHNGMKQISAN-RPLLKPEDAKGLKFRIQASDILAAQF 179 G GQ +L +E F GLA+ NG + ++ N RP+ D GLK R+ AS + + + Sbjct: 119 DGPLGQQILTELEQVGFKGLAFSENGFRNLTNNRRPVQAAADVSGLKIRVMASPLHKSIW 178 Query: 180 QGLNATPQKLAFSEVYQALQVGTVDGQENTWSNIFSQKFYEVQKDITESDHGVIDYMVVV 239 Q L A P + + +Y L+ G +DGQEN + KFYEVQ ++ + H ++ V Sbjct: 179 QALGANPTPMPW-PIYSELEQGVIDGQENPLWVMEVYKFYEVQNYMSMTRHVYSAHIDVA 237 Query: 240 NAKWWNGLSKDLQDAMKKAMDEA 262 + WW GL+ Q+ ++ AM +A Sbjct: 238 SLLWWQGLTTADQEMIRSAMQQA 260 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: 229 Number of extensions: 9 Number of successful extensions: 3 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: 325 Length adjustment: 28 Effective length of query: 304 Effective length of database: 297 Effective search space: 90288 Effective search space used: 90288 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 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