Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc04257 (305 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 144 bits (364), Expect = 2e-39 Identities = 90/280 (32%), Positives = 154/280 (55%), Gaps = 22/280 (7%) Query: 32 VYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPL---EITFEPWVKAWAEACTG 88 + G L+V+AL L PL M+ S+ E F PPL +TF + + +A G Sbjct: 15 INGGLLVLALVSLAPLLWMVSVSVMPAGE---ATTFPPPLTPSHVTFANYHELFARTGMG 71 Query: 89 LNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILIVGAFIPYQV 148 +N F NS+ ++V + S+ + ++ GYA A RF G D F +L+ IP QV Sbjct: 72 VN-------FANSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQV 124 Query: 149 MIYPIVIVLREMGVYGTLTGLII--VHTIFGMPILTLLFRNYFAGLPEELFKAARVDGAG 206 + P+ ++++++G+ + G+I+ + T+FG+ L R Y +P+EL +AAR+DGAG Sbjct: 125 AMLPLFLLMKQLGLVNSFGGVIVPALATVFGI----FLVRQYARSIPDELLEAARMDGAG 180 Query: 207 FWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFG-VVFTRPEYYPMTVQLNNIVNSVQG 265 I+F+I+LPM P+ V I G WNDF++ +V T E+Y + V L + S + Sbjct: 181 EMRIFFQIVLPMLKPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATL--SREH 238 Query: 266 VKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 + + + MA ++T + L ++ + R +++G+ G+VKG Sbjct: 239 IMDVEMMMAGAVVTVIPVLALFLLLQRYYIQGLMLGSVKG 278 Lambda K H 0.329 0.145 0.450 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: 215 Number of extensions: 10 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: 305 Length of database: 278 Length adjustment: 26 Effective length of query: 279 Effective length of database: 252 Effective search space: 70308 Effective search space used: 70308 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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