Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_152471781.1 CDO52_RS22265 ABC transporter permease subunit
Query= uniprot:A8LLL5 (334 letters) >NCBI__GCF_002263495.1:WP_152471781.1 Length = 265 Score = 91.3 bits (225), Expect = 2e-23 Identities = 73/246 (29%), Positives = 113/246 (45%), Gaps = 31/246 (12%) Query: 91 WVGLDNYAQMASE---PKFWEAMRNNMFWLIVVPALSTAFGLLAAQLTDRIKWGN-VAKS 146 + GLDN+A + S + W A +N+ + + T GL A L + G ++ Sbjct: 12 FAGLDNFAHLFSGVYGDRLWRAFGHNLAFFAGTMLVQTTLGLAFAVLLRHTRAGRRFLQT 71 Query: 147 IIFMPMAISFVGASVIWKLVYDGRPIEQEQIGILNAIIVGLG---------GDPVTFLTI 197 +P +S + +W L+ Q G +NA + +G GDP L + Sbjct: 72 AYVLPHLVSPIVVGYLWSLMLS------PQFGAVNAALRAVGLDALAQPWTGDPA--LAL 123 Query: 198 PFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIIDGASPLQIFFKIKVPQIMP 257 P L++V W GF M++ SAAL GIP E EAA +DGAS Q F + +P +MP Sbjct: 124 PT-----LILVNAWQWIGFPMLLFSAALAGIPPEYEEAARVDGASGWQAFRTVTLPLLMP 178 Query: 258 TVVVVWTTITLVVLKVFDIVFAMTNGQ----WETQVLANYMFDKLFRANDWG-VGSASAM 312 + +V + + V D+V+AM Q T VL + F D G +G ASA+ Sbjct: 179 AIGIVTVLTFIGNMNVLDLVYAMQGSQGAPAGATDVLGLLFYRTAFNNPDPGAIGQASAL 238 Query: 313 VIMLLV 318 +++ V Sbjct: 239 AVVMFV 244 Lambda K H 0.329 0.143 0.455 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: 200 Number of extensions: 13 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: 334 Length of database: 265 Length adjustment: 26 Effective length of query: 308 Effective length of database: 239 Effective search space: 73612 Effective search space used: 73612 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 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