Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate GFF1859 Psest_1898 ABC-type sugar transport system, permease component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >FitnessBrowser__psRCH2:GFF1859 Length = 280 Score = 485 bits (1248), Expect = e-142 Identities = 230/272 (84%), Positives = 254/272 (93%) Query: 10 ISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDV 69 ++ R+ IYATLLLA AVYL+PL+VMLLTSFK+PEDIRTGNLLSWP +GW+ AWD Sbjct: 9 LTLGRLTIYATLLLACAVYLVPLIVMLLTSFKTPEDIRTGNLLSWPEAFSAMGWLTAWDS 68 Query: 70 VGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPA 129 +GGYFWNSVKI +PAVLIST +GA+NGYVLSMWRFRGSQLFFGLLLFGCFLPFQ +LLPA Sbjct: 69 IGGYFWNSVKIVIPAVLISTALGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQVILLPA 128 Query: 130 SFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLK 189 SFTLGK GLANTTTGLVLVHVVYGLAFTTLFFRN+YVS+PDALV+AARLDGAGFFTIF + Sbjct: 129 SFTLGKLGLANTTTGLVLVHVVYGLAFTTLFFRNFYVSVPDALVRAARLDGAGFFTIFGR 188 Query: 190 ILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAKEYNVDM 249 ILLPMS+PI+MVCLIWQFTQIWNDFLFGVVFASGD QP+TVALNNLVNTSTGAK+YNVDM Sbjct: 189 ILLPMSVPIIMVCLIWQFTQIWNDFLFGVVFASGDTQPVTVALNNLVNTSTGAKQYNVDM 248 Query: 250 AAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 AAAMIAGLPTL+VY+ AGKYFLRGLT+GAVKG Sbjct: 249 AAAMIAGLPTLVVYVVAGKYFLRGLTAGAVKG 280 Lambda K H 0.329 0.143 0.447 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: 370 Number of extensions: 6 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: 281 Length of database: 280 Length adjustment: 26 Effective length of query: 255 Effective length of database: 254 Effective search space: 64770 Effective search space used: 64770 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: 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