Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_011913471.1 PST_RS11845 cystine ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >NCBI__GCF_000013785.1:WP_011913471.1 Length = 222 Score = 71.2 bits (173), Expect = 2e-17 Identities = 35/89 (39%), Positives = 57/89 (64%) Query: 238 VLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQAL 297 + + L A + ++ AA+ AEI+R+ I S+ GQ EAA S+G+ TL + I+PQA Sbjct: 84 IQLDPLPAALIGFSLNMAAYTAEILRAAIASIDRGQWEAAASIGMGRAQTLYRAILPQAA 143 Query: 298 RVIIPPLTSQYLNLAKNSSLAAGIGYPEM 326 R +PPL + +++L K+++LAA I PE+ Sbjct: 144 RTALPPLGNSFISLVKDTALAATIQVPEL 172 Score = 40.8 bits (94), Expect = 4e-08 Identities = 19/57 (33%), Positives = 32/57 (56%) Query: 73 TLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILFWYFAV 129 T++++ G+ +LGF + + RL W + LA VYV FR P L+Q+ Y+ + Sbjct: 23 TVVLSLSGMFFGLLLGFGLALLRLYAFWPLQWLARVYVSFFRGTPLLVQLFMIYYGL 79 Lambda K H 0.328 0.141 0.430 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: 209 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 222 Length adjustment: 26 Effective length of query: 349 Effective length of database: 196 Effective search space: 68404 Effective search space used: 68404 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 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