Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate YP_004144834.1 Mesci_5724 polar amino acid ABC transporter inner membrane subunit
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >NCBI__GCF_000185905.1:YP_004144834.1 Length = 324 Score = 127 bits (320), Expect = 2e-34 Identities = 71/217 (32%), Positives = 117/217 (53%), Gaps = 1/217 (0%) Query: 2 NYQLNFAAVWRDFDTLLA-GLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVY 60 ++ L+ +W + L+ G + ++ VS+ +I + A A LS + +AS Y Sbjct: 103 SFNLSMPFIWENLPYLITQGAVTTIYISAVSLIFASIIAMIAAIAKLSSNGFAYAIASFY 162 Query: 61 VTVIRNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQ 120 + R P+LV I LIY LP LGI ++ +PS V+ LSL GAY+TE+FR G+ SI +GQ Sbjct: 163 TSFFRGLPLLVQIYLIYLGLPQLGIFINAVPSGVLALSLCTGAYMTEIFRAGIQSIDRGQ 222 Query: 121 REAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKI 180 EA ++G G + +P L ++P + N FIS+ KD+SL + + V ELT+ AR + Sbjct: 223 WEASRSMGFGFGLTMRRIILPQALPVIIPPMGNTFISMLKDSSLVSILGVWELTFLARTL 282 Query: 181 NVESYRVIETWLVTTALYVAACYLIAMVLRYFEQRLA 217 +++ +E + +Y + +V E+ A Sbjct: 283 GQPTFQHMEMLITAAIIYWIMSICLELVQSRIERHFA 319 Lambda K H 0.329 0.142 0.414 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: 182 Number of extensions: 6 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: 324 Length adjustment: 25 Effective length of query: 195 Effective length of database: 299 Effective search space: 58305 Effective search space used: 58305 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