Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate WP_152471781.1 CDO52_RS22265 ABC transporter permease subunit
Query= reanno::Smeli:SMc02872 (315 letters) >NCBI__GCF_002263495.1:WP_152471781.1 Length = 265 Score = 193 bits (491), Expect = 3e-54 Identities = 109/256 (42%), Positives = 149/256 (58%), Gaps = 6/256 (2%) Query: 55 QLTFVGLGNFKVLFGDPRWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRFG 114 +L F GL NF LF + W A +N FF M VQ +G+A A +L R G Sbjct: 9 RLGFAGLDNFAHLFSGV-YGDRLWRAFGHNLAFFAGTMLVQTTLGLAFAVLLR--HTRAG 65 Query: 115 A-FYRTAIFLPTLLSFVIVGFIWKLILSPIWGVAPYLLDTVGLRSLFGPWLGKPDTALIA 173 F +TA LP L+S ++VG++W L+LSP +G L VGL +L PW G P AL Sbjct: 66 RRFLQTAYVLPHLVSPIVVGYLWSLMLSPQFGAVNAALRAVGLDALAQPWTGDPALALPT 125 Query: 174 VSLISVWQYIGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSI 233 + L++ WQ+IG PM+L AAL IP E EAA +DG +GW F + LPL++PAIGIV++ Sbjct: 126 LILVNAWQWIGFPMLLFSAALAGIPPEYEEAARVDGASGWQAFRTVTLPLLMPAIGIVTV 185 Query: 234 LTFVGNFNAFDLIYTVQGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFL 293 LTF+GN N DL+Y +QG+ P +TD+LG L YRT F G + +A +MF+ Sbjct: 186 LTFIGNMNVLDLVYAMQGSQGAPAGATDVLGLLFYRTAFN-NPDPGAIGQASALAVVMFV 244 Query: 294 IILAGVALYLFGIQRR 309 I GV++ + RR Sbjct: 245 FIF-GVSIAATRVLRR 259 Lambda K H 0.331 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: 318 Number of extensions: 17 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: 315 Length of database: 265 Length adjustment: 26 Effective length of query: 289 Effective length of database: 239 Effective search space: 69071 Effective search space used: 69071 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 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