Align TRAP dicarboxylate transporter DctP subunit; Flags: Precursor (characterized, see rationale)
to candidate RR42_RS35000 RR42_RS35000 ABC transporter substrate-binding protein
Query= uniprot:Q2IUT5 (332 letters) >FitnessBrowser__Cup4G11:RR42_RS35000 Length = 315 Score = 101 bits (251), Expect = 3e-26 Identities = 79/267 (29%), Positives = 126/267 (47%), Gaps = 4/267 (1%) Query: 8 VASIAALALVGPAAAQQPIVVKFSHVVADNTPKGQAAIKFKELAEKYTNGKVKVEVYPNS 67 +A+ A G A AQ + K++HV + P + ++ E K +NG+ +++V+P S Sbjct: 1 MATCVASLACGGALAQTKL--KWAHVYETSEPFHKWSVWAAEEIRKRSNGRYQIDVFPAS 58 Query: 68 QLFGDAKEMEAVALGDVQFIAPSLSKFDKFTKQIQVFDLPFLFNDIAAVDRFQAGKQGQA 127 QL + + +A+G V I S K +I V P+ F D + + + Sbjct: 59 QLGKENDINQGLAMGSVDIIISGSSFAAKSFPRIGVTYYPYTFRDANHLLAYTKSDIYKE 118 Query: 128 LLRSMESKNFLGL-AYWHNGMKQISANRPLLKPEDAKGLKFRIQASDILAAQFQGLNATP 186 L R E K+ + A + G +Q ++N+P + KGLK R+ A + Sbjct: 119 LTRGYEEKSGNHIVATTYYGTRQSTSNKPFSHCAEMKGLKMRVPDVPAYLAMPRACGVNT 178 Query: 187 QKLAFSEVYQALQVGTVDGQENTWSNIFSQKFYEVQKDITESDHGVIDYMVVVNAKWWNG 246 +AF+EVY ALQ GTV+ QEN I ++KFYEVQK I + H V V++ W Sbjct: 179 SPIAFAEVYLALQNGTVEAQENPLPTIEAKKFYEVQKYIVLTGHIVDHLNTVISGGLWKK 238 Query: 247 LSK-DLQDAMKKAMDEATKVNNDVAGK 272 LS+ D + A + A + DV + Sbjct: 239 LSEADRKMFSDVAQEAAMRATADVVAR 265 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: 205 Number of extensions: 4 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: 315 Length adjustment: 28 Effective length of query: 304 Effective length of database: 287 Effective search space: 87248 Effective search space used: 87248 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: 48 (23.1 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