Align LacG, component of Lactose porter (characterized)
to candidate SM_b20969 SM_b20969 sugar uptake ABC transporter permease
Query= TCDB::P29824 (273 letters) >FitnessBrowser__Smeli:SM_b20969 Length = 270 Score = 136 bits (342), Expect = 5e-37 Identities = 80/262 (30%), Positives = 135/262 (51%), Gaps = 3/262 (1%) Query: 13 VQYSVLSLAAFLSIFPFIWMVIGTTNTTSQIIRGKVTFGTALF--DNIASFFAQVDVPLV 70 V Y+ L L + L I PF W + +T+++ R + + +N A+ +++ Sbjct: 5 VLYATLILLSALFIAPFYWTFMTAVKSTAELYRFPPVLWPSEWHWENFAAAWSKQPFGTY 64 Query: 71 FWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFAALMIPLFMLM 130 NS+ + ++ T LL SSL +GF FR R+ ++ ++L T+M+P+ MIPL+M Sbjct: 65 LSNSLIVVVLSTIGQLLSSSLVAFGFARFRFPGRDALFVLLLATMMIPWDVKMIPLYMEF 124 Query: 131 GQAGLLNTHIAIMLPM-IASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQIFFYIYVPV 189 G +NT +++P A AF +F RQ P E+ +AA++DG + I++ I++P+ Sbjct: 125 NMLGWINTLKPLIVPAYFADAFFVFLLRQYIMTIPMEIDEAARMDGANSFDIYWRIHLPL 184 Query: 190 MRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASAYSPEYGTVMIGTILA 249 M FM WN+YL PLI L T+TL +S + + ++ T++ Sbjct: 185 MLPALVLVGTFHFMNAWNDYLGPLIFLNDQSKYTLTLGLSMFKGLHEIDVTSIAAITVIL 244 Query: 250 TLPTLLVFFAMQRQFVQGMLGS 271 LP L +FF QR + G +GS Sbjct: 245 CLPPLALFFLAQRYIMDGAVGS 266 Lambda K H 0.331 0.140 0.416 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: 18 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: 273 Length of database: 270 Length adjustment: 25 Effective length of query: 248 Effective length of database: 245 Effective search space: 60760 Effective search space used: 60760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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