Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like
Query= uniprot:A3DHA2 (303 letters) >FitnessBrowser__SynE:Synpcc7942_0471 Length = 276 Score = 129 bits (323), Expect = 1e-34 Identities = 81/281 (28%), Positives = 141/281 (50%), Gaps = 20/281 (7%) Query: 26 VYVILIVITVVLLFPILFTIANSFMSDKEVLDTYQKKIEEVEEGESTEFLGFKLIPDMVS 85 +Y++L I V +L P+L+ ++ +F S E + + + +P + Sbjct: 12 LYLLLGTIAVAMLIPLLWLVSTAFKSAGEDIFQFPPQF----------------LPTQPT 55 Query: 86 MKQYYTVLFRKPTFLLMFLNSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKLFFVFIV 145 + + V P FLNS + + V + ++ AAY A+L F R LF + + Sbjct: 56 LDNFRRVWTENPLGQY-FLNSTWVALLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVA 114 Query: 146 VMLMPLQVTLVPNYILLRKLDMIGSFLSVILPGGFSAFGVVLLRQYMRGIPDECCEAAMI 205 +L+P QV ++P Y+L+ L + ++L ++ P SAFG+ LLRQ +GIP + EAA I Sbjct: 115 TILIPFQVVMIPLYVLIINLGLRNTYLGLVFPYLASAFGIFLLRQAFQGIPKDLEEAARI 174 Query: 206 DGAGYLKTFTKIILPQCKSIIASLAILAFIDNWNMVEQPLIFLSDSAKYPLSVYLAYINE 265 DG L + +++P + + +LAI FI +W+ PLI L + +Y L + +A + Sbjct: 175 DGCNDLGVWWNVMIPSARPALITLAIFVFIGSWSDFLWPLIILDEPDRYTLPLGIATLAS 234 Query: 266 G---DLGLAFASGVLYMIPTVLIYLYGEKYFVEGIQLTGIK 303 G D L A VL ++P ++L ++Y V +G+K Sbjct: 235 GFSLDWRLVAAGSVLSILPVFGVFLALQRYIVPSAAASGVK 275 Lambda K H 0.331 0.147 0.425 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: 216 Number of extensions: 10 Number of successful extensions: 2 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: 303 Length of database: 276 Length adjustment: 26 Effective length of query: 277 Effective length of database: 250 Effective search space: 69250 Effective search space used: 69250 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: 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