Align ABC transporter permease (characterized, see rationale)
to candidate WP_013420532.1 RVAN_RS14865 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000166055.1:WP_013420532.1 Length = 302 Score = 152 bits (384), Expect = 9e-42 Identities = 92/303 (30%), Positives = 161/303 (53%), Gaps = 21/303 (6%) Query: 3 ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62 + Q + +G+ +G +YA IA GY + + + +NF GE LM+GA+ + + P Sbjct: 15 VFWQLVASGVAVGMIYATIAFGYQLTFATSKTLNFGQGEALMLGAMLGLTLL-------P 67 Query: 63 GAPGWVILLLATIIACVVAATLNFVIEKVAYRP-LRSSPRLAPLITAIGMSILLQTLAMI 121 W++L + I A V+E++ RP + + ++ I + I+ + +A Sbjct: 68 YLGYWLMLPVILIFGMAQGA----VVERLGVRPAIETKSEFGWIMATIALGIIFRNMAEN 123 Query: 122 IWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATA 181 IW + +P+ LP + E+G I P +I+++ + +A++ + G+A AT+ Sbjct: 124 IWGRDDLKFPSPLPETAIELGAVRILPAEIMVVVGALLMMAAVETFNRRSIYGKAFVATS 183 Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241 + A LMG+ VI+ ++ + ++ AA AG++ A T TMG + LKAF A+ Sbjct: 184 NDIDAAGLMGIDTRRVITMSYAMSSMTAAFAGVLVAPVTLTGA-TMGAVLALKAFAVAII 242 Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLL 301 GG+ + GA+VGGILLG+IE TLTG + + Y D+ I+++I+L +RP+GL Sbjct: 243 GGLDSALGAIVGGILLGVIE--------TLTGYYVSTGYKDVPGLILVLIVLAIRPAGLF 294 Query: 302 GER 304 G R Sbjct: 295 GRR 297 Lambda K H 0.327 0.142 0.419 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: 221 Number of extensions: 15 Number of successful extensions: 4 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: 309 Length of database: 302 Length adjustment: 27 Effective length of query: 282 Effective length of database: 275 Effective search space: 77550 Effective search space used: 77550 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 (21.7 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