Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate CCNA_01507 CCNA_01507 cystine transport system permease protein
Query= reanno::pseudo3_N2E3:AO353_21720 (220 letters) >FitnessBrowser__Caulo:CCNA_01507 Length = 219 Score = 104 bits (259), Expect = 1e-27 Identities = 59/194 (30%), Positives = 102/194 (52%) Query: 25 SVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLACFYMAPAL 84 ++ SV+ + +G ++G + L+ + +R P YV RGTP+ V + +Y P Sbjct: 22 TIVLSVIGMSIGVVLGFLLALMRLSRSALLRWPAGVYVSAFRGTPLLVQLFLIYYGLPQF 81 Query: 85 GWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQALAYVLLPQA 144 G ++ A +G +L ++ EI+R A+ A+ +GQ EA+ +G++ Q L V+LPQA Sbjct: 82 GLEMPPLVAAGIGFSLNVAAYSCEILRSAIAAVDKGQWEAASVLGMSRGQTLRRVILPQA 141 Query: 145 LRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLFFIINY 204 R + NS +VK ++L + I V EL Q I ART+ YL A +++I++ Sbjct: 142 ARTAVAPLSNSFISLVKDTSLAATIQVPELFRQAQLITARTYEIFTLYLAAAAIYWILST 201 Query: 205 AIELLGRHIEKRVA 218 + +E+R A Sbjct: 202 ILAAAQTRLERRAA 215 Lambda K H 0.330 0.142 0.440 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: 113 Number of extensions: 7 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: 220 Length of database: 219 Length adjustment: 22 Effective length of query: 198 Effective length of database: 197 Effective search space: 39006 Effective search space used: 39006 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 (21.9 bits) S2: 45 (21.9 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