Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate BPHYT_RS29185 BPHYT_RS29185 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__BFirm:BPHYT_RS29185 Length = 314 Score = 263 bits (673), Expect = 3e-75 Identities = 121/275 (44%), Positives = 183/275 (66%) Query: 23 LVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDRWWVASKNLA 82 L L P ++ V+ + G ++WT +S +NS PS + G QY RL +NDRW ++ +N+ Sbjct: 33 LALLPMVMTVVFAYLGTMVWTARVSLSNSRTFPSGDFAGFTQYARLFNNDRWLLSLQNIV 92 Query: 83 LFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWLLNPGLGL 142 ++G FI +V+G+ LA+ +DQR+ EG +RTV+LYP A+S + TG W+W+LNP LG Sbjct: 93 IYGACFIVACMVIGLLLAIFIDQRVVAEGALRTVFLYPYAMSFVATGLVWQWILNPELGA 152 Query: 143 DKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQSIIRAAQV 202 +L G+ R DW+VDQD V+Y +VIA VWQASG VMA+ LAGLRG+D + +AA++ Sbjct: 153 QAVLHKLGFAHARFDWIVDQDWVIYTIVIATVWQASGLVMALLLAGLRGIDDELWKAARI 212 Query: 203 DGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYS 262 DG +Y+ IV+P L P +AF++L + +K +D V AMT GGPG +S++PA F+ Sbjct: 213 DGIPRWRVYVSIVVPMLGPSISTAFVLLFVMVVKLYDAVVAMTQGGPGTASEVPAKFIMD 272 Query: 263 FTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELR 297 + F R +G+ SA+++++L VL IL P+ Y+ R Sbjct: 273 YLFGRANIGLASAASIVLLATVLAILAPFFYARSR 307 Lambda K H 0.329 0.141 0.448 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: 340 Number of extensions: 11 Number of successful extensions: 1 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: 302 Length of database: 314 Length adjustment: 27 Effective length of query: 275 Effective length of database: 287 Effective search space: 78925 Effective search space used: 78925 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 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