Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_084164874.1 N825_RS19120 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >NCBI__GCF_000576635.1:WP_084164874.1 Length = 288 Score = 104 bits (260), Expect = 3e-27 Identities = 71/230 (30%), Positives = 125/230 (54%), Gaps = 11/230 (4%) Query: 151 LDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVL-LAVVVG 209 LDNY EVL + S NS+ +AV +T++ + + AAYALA F + L + Sbjct: 68 LDNYFEVLFNRDVLSSLTNSIIIAVSTTILAVGLGTPAAYALARFEFKSKEELWFWFITN 127 Query: 210 LLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPRE 269 ++ P+ ++L P+ + + T++ + L + F LP+ +++ + G+P++ Sbjct: 128 RMLSPIVVAL-PIFLMARTLNLI-----DTHIVLILVYLTFNLPIVVWICTDQFRGVPKD 181 Query: 270 IMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLT 329 + E+AR+ GAS F IF +I LPL+ P +A AIF F+++WN+LL A+V + Sbjct: 182 LDEAARLAGASRFTIFWRIALPLAMPGVAVSAIFSFIFSWNELLYALVL--TRNVARTAP 239 Query: 330 GRLVNLLGSRGGNWEILTASAFITIVVPLIVF-FALQRYLVRGLLAGSVK 378 + + W + A+ + IV+P+IVF + ++LV+GL G+VK Sbjct: 240 VAATSFMSGYDLPWGEIMATGTL-IVLPVIVFALIVSKHLVQGLTMGAVK 288 Lambda K H 0.324 0.139 0.418 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: 243 Number of extensions: 14 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: 380 Length of database: 288 Length adjustment: 28 Effective length of query: 352 Effective length of database: 260 Effective search space: 91520 Effective search space used: 91520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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