Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate H281DRAFT_01453 H281DRAFT_01453 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::WCS417:GFF4323 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_01453 Length = 319 Score = 261 bits (667), Expect = 1e-74 Identities = 119/275 (43%), Positives = 184/275 (66%) Query: 23 LVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWWVASKNLA 82 L L P + V+ + G ++WT +S +NS P+ +AGL QY RLF+N RW ++ +N+ Sbjct: 38 LALLPMILTVVFAYLGTMVWTARVSLSNSRTFPSGDFAGLTQYVRLFNNARWLLSLQNIV 97 Query: 83 VFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGL 142 ++G FI +VIG+ LAIF+DQ++ EG +RT++LYP A+S + TG W+W+LNP +G Sbjct: 98 IYGACFIVACMVIGLLLAIFIDQRVVAEGALRTVFLYPYAMSFVATGLVWQWILNPELGA 157 Query: 143 DKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQI 202 +L G+ R DW++D D +Y +VIA VWQASG +MA+ LAGLRG+D + +AA+I Sbjct: 158 QAVLHKLGFVHARFDWIVDQDWAIYTIVIATVWQASGLVMALLLAGLRGIDDELWKAARI 217 Query: 203 DGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYS 262 DG R+Y S+V+P L P +A ++L + +K +D V AMT GGPG +S++PA F+ Sbjct: 218 DGIPRWRVYASIVVPMLGPSISTAFVLLFVMVVKLYDAVVAMTQGGPGTASEVPAKFIMD 277 Query: 263 FTFSRGQMGMGSASAILMLGAILAIIVPYLYSELR 297 + F R +G+ SA++I++L +LAI+ P+ Y+ R Sbjct: 278 YLFGRANIGLASAASIVLLATVLAILTPFFYARSR 312 Lambda K H 0.330 0.141 0.455 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: 331 Number of extensions: 15 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: 319 Length adjustment: 27 Effective length of query: 275 Effective length of database: 292 Effective search space: 80300 Effective search space used: 80300 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