Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 103 bits (258), Expect = 5e-27 Identities = 69/212 (32%), Positives = 109/212 (51%), Gaps = 8/212 (3%) Query: 168 LNSLTVAVPSTVIPILIAAFAAYALAWMPFPG-RAVLLAVVVGLLVVPLQMSLIPLLQLY 226 LN++ V+ ST + + AAYA+ + F G + V LAV + L+ P + IPL + Sbjct: 90 LNTVIVSTISTFASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLIPP-SILFIPLASIV 148 Query: 227 NGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFV 286 +G F T + L + F +P +LL Y +P E+ E A +DGA+ ++I V Sbjct: 149 FQLGLF-----DTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILV 203 Query: 287 KIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEIL 346 KIILPL+ P L S IF F +WN+ + A+ F+ + + K V G + L+ +W L Sbjct: 204 KIILPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELIEGDVYHWGAL 263 Query: 347 TASAFITIVVPLIVFFALQRYLVRGLLAGSVK 378 A A + + +V+ Y V G + G+VK Sbjct: 264 MAGALLGSLPVALVYSFFVEYYVSG-MTGAVK 294 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: 239 Number of extensions: 8 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: 380 Length of database: 295 Length adjustment: 28 Effective length of query: 352 Effective length of database: 267 Effective search space: 93984 Effective search space used: 93984 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 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