Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_013403896.1 CALHY_RS10330 carbohydrate ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >NCBI__GCF_000166355.1:WP_013403896.1 Length = 275 Score = 147 bits (371), Expect = 2e-40 Identities = 86/264 (32%), Positives = 140/264 (53%), Gaps = 2/264 (0%) Query: 7 YGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWE-AFRPKFQN 65 + FL + +P + T+LK + + WQ P P ++ T +E +F +N Sbjct: 12 FAFLAIWTLIADIPFLFMAFTSLKTQMELLMGNTWQIPKKPTIGNYLTVFEGSFFNYLKN 71 Query: 66 SVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSI 125 SV+ + +L LV S+ +V A+ F + +L++LI+ GM IP LIP++ + Sbjct: 72 SVIAVSVSVVLILLVSSMAAFVFARMKFGLNNVLYSLIIAGMAIPIHVTLIPIYILTNKM 131 Query: 126 GLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSV 185 +Y S+ L+ +V +P+ I + EIP EL EAA+IDG F ++ ++ILPLS Sbjct: 132 KIYDSILALIGPYVALSLPMSIFILTEFMREIPIELEEAAKIDGCSMFRLYSNIILPLSR 191 Query: 186 PAFVVVAIWQFTQIWNEFLFAVTLT-RPESQPITVALAQLAGGEAVKWNLPMAGAILAAL 244 PA + V I+ T +WNEF+FA+ LT PE + + + + MA L+ L Sbjct: 192 PALITVGIYNGTYLWNEFIFALVLTSTPEKRTLPLGIWDFQTKYGSDIPAIMAFLTLSLL 251 Query: 245 PTLLVYILLGRYFLRGLLAGSVKG 268 P L+ YIL ++G++AG+VKG Sbjct: 252 PMLIAYILGQDKIIKGMMAGAVKG 275 Lambda K H 0.330 0.146 0.461 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: 254 Number of extensions: 15 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: 268 Length of database: 275 Length adjustment: 25 Effective length of query: 243 Effective length of database: 250 Effective search space: 60750 Effective search space used: 60750 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 24 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