Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like
Query= uniprot:A8LLL4 (385 letters) >lcl|FitnessBrowser__SynE:Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like Length = 276 Score = 113 bits (283), Expect = 6e-30 Identities = 72/238 (30%), Positives = 119/238 (50%), Gaps = 13/238 (5%) Query: 153 PPEF-----TFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWME 207 PP+F T N+ + + + + F N+ V + + +L + AAY LA +E Sbjct: 46 PPQFLPTQPTLDNFRRVWTE----NPLGQYFLNSTWVALLTVGLNLLFCSLAAYPLARLE 101 Query: 208 FPGRALLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRN 267 F GR L LIV +++P Q+ +IPL L +G+ YLG L I+LLR Sbjct: 102 FKGRQTLFLLIVATILIPFQVVMIPLYVLIINLGLRNTYLG--LVFPYLASAFGIFLLRQ 159 Query: 268 YMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLID 327 G+P+D+ E A++DG D ++ +++P + PAL + AIF F+ +W+D L + L + Sbjct: 160 AFQGIPKDLEEAARIDGCNDLGVWWNVMIPSARPALITLAIFVFIGSWSDFLWPLIILDE 219 Query: 328 ATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 T + I L +W ++A + +SI VF ++QR++V A VK Sbjct: 220 PDRYTLPL--GIATLASGFSLDWRLVAAGSVLSILPVFGVFLALQRYIVPSAAASGVK 275 Lambda K H 0.323 0.138 0.419 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: 286 Number of extensions: 20 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: 385 Length of database: 276 Length adjustment: 28 Effective length of query: 357 Effective length of database: 248 Effective search space: 88536 Effective search space used: 88536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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