Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 140 bits (354), Expect = 3e-38 Identities = 85/238 (35%), Positives = 131/238 (55%), Gaps = 14/238 (5%) Query: 145 TPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLL 204 TP T NY E+ + G+G +F NSL V+V T+ +L+ A YA A + F GR L Sbjct: 52 TPSHVTFANYHELFARTGMGVNFANSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLF 111 Query: 205 AVVVGLLVVPLQMSLIPLLQLYNGVG---AFFGVSAKTYMGIWLAHTGFGLPLAIYLLRN 261 V++ LV+P Q++++PL L +G +F GV T FG I+L+R Sbjct: 112 QVLMAALVIPAQVAMLPLFLLMKQLGLVNSFGGVIVPALA------TVFG----IFLVRQ 161 Query: 262 YMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGA 321 Y +P E++E+AR+DGA + IF +I+LP+ P L + +IF F+ WND + ++ L Sbjct: 162 YARSIPDELLEAARMDGAGEMRIFFQIVLPMLKPVLVTLSIFTFMGAWNDFMWPLIVL-T 220 Query: 322 GDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379 + L L L + E++ A A +T++ L +F LQRY ++GL+ GSVKG Sbjct: 221 DQEHYTLPVALATLSREHIMDVEMMMAGAVVTVIPVLALFLLLQRYYIQGLMLGSVKG 278 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: 272 Number of extensions: 18 Number of successful extensions: 4 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: 380 Length of database: 278 Length adjustment: 28 Effective length of query: 352 Effective length of database: 250 Effective search space: 88000 Effective search space used: 88000 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: 48 (23.1 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