Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 75.1 bits (183), Expect = 2e-18 Identities = 41/127 (32%), Positives = 71/127 (55%) Query: 91 FQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQSLGYVLLPQALRQILP 150 F A +LGL + G+ + EI+RG + ++P GQ EA+ A+GLT Q+L +++PQALR I+P Sbjct: 245 FTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVP 304 Query: 151 TWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLFFIINYAIELLG 210 + + K S+L +G +L + Q + +T +E +L + IN I Sbjct: 305 SLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGM 364 Query: 211 RHIEKRV 217 +++R+ Sbjct: 365 NGLQQRL 371 Score = 34.7 bits (78), Expect = 3e-06 Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 2/63 (3%) Query: 18 LWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWM-RAPFRFYVDLIRGTPVFVLVLA 76 L G + S++ + ++L T+IG +AG V + W+ R R YV ++R TP+ + ++ Sbjct: 82 LVVGLVNSLRVIAIGLILTTVIGTLAG-VAAFSENWLLRQLSRGYVAVVRNTPLLLQLIV 140 Query: 77 CFY 79 ++ Sbjct: 141 WYF 143 Lambda K H 0.330 0.142 0.443 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: 267 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 220 Length of database: 377 Length adjustment: 26 Effective length of query: 194 Effective length of database: 351 Effective search space: 68094 Effective search space used: 68094 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