Align ABC transporter permease (characterized, see rationale)
to candidate WP_086511130.1 BZY95_RS17255 sugar ABC transporter permease
Query= uniprot:A0A166QFV1 (320 letters) >NCBI__GCF_002151265.1:WP_086511130.1 Length = 296 Score = 134 bits (337), Expect = 3e-36 Identities = 95/288 (32%), Positives = 149/288 (51%), Gaps = 19/288 (6%) Query: 35 PMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNGSSWSGILVDPQWWN 94 P + L L PL T WFSL NL F G NY F + DP W Sbjct: 22 PAVTLLLLWMLVPLGMTVWFSLQRYNLLMPEMVGFAGLENYEF--------LFTDPALWR 73 Query: 95 AVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWAIPTIVSAKIW-SWM 153 A+ NTL + + VV G+L+A+L +F GR + R L + P+ + VSA +W + M Sbjct: 74 AMGNTLVLVGSVLTITVVGGVLLAVLFQQEFPGRGIARVLAISPFFVMPTVSALVWKNMM 133 Query: 154 LNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLAALQMLPS 213 ++ G++ L GL + W + L M ++II+ W+ +PF L++L A+Q L Sbjct: 134 MHPSNGVLAWLAGVFGL--PAVDWFSA--LPMTSIIIIVAWQWLPFALLILLTAMQSLDE 189 Query: 214 DCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSN----SSS 269 D EAAR+DG P+ VF+ +TLP L A+ V + +++ L +F IYV TS +++ Sbjct: 190 DQVEAARMDGAGPIAVFFYITLPHLKRAISVVIMIQMIFLLTIFAEIYVTTSGGPGLATT 249 Query: 270 TMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGRRQLE 317 ++ +Y Q L++F DVG SA + ++ ++A+ + L R LE Sbjct: 250 NLAFLIY-MQALLDF-DVGLASAGGVVAIILANIVAIFLVRLVARNLE 295 Lambda K H 0.329 0.140 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: 229 Number of extensions: 16 Number of successful extensions: 3 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: 320 Length of database: 296 Length adjustment: 27 Effective length of query: 293 Effective length of database: 269 Effective search space: 78817 Effective search space used: 78817 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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