Align ABC transporter permease (characterized, see rationale)
to candidate WP_028999461.1 H537_RS0121280 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000430725.1:WP_028999461.1 Length = 307 Score = 470 bits (1209), Expect = e-137 Identities = 232/309 (75%), Positives = 273/309 (88%), Gaps = 2/309 (0%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MDI LQQIINGLVLGSMYAL+ALGYTMVYGII LINFAHGEVLM+GA+ SW+ + ++ + Sbjct: 1 MDIFLQQIINGLVLGSMYALVALGYTMVYGIINLINFAHGEVLMVGAMVSWTVVTVLGDS 60 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 G PGW+++L++ I A V+ + LNF IEK+AYRPLR++PRLAPLITA+GMS+LLQTLAM Sbjct: 61 --GLPGWLLMLISLICAVVICSALNFTIEKLAYRPLRNAPRLAPLITAMGMSLLLQTLAM 118 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 IIWKPN KP+P +LP+ P EI GA I+ TQILILG+TA+ LA+L+YLVN T LGRAMRAT Sbjct: 119 IIWKPNPKPFPQLLPTDPIEIAGAVISVTQILILGITALVLAALLYLVNKTKLGRAMRAT 178 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 AENPRVASLMGV+PD VISATFIIGA LAA+AGIM+A+NYGT QHTMGFLPGLKAFTAAV Sbjct: 179 AENPRVASLMGVRPDWVISATFIIGASLAALAGIMWAANYGTVQHTMGFLPGLKAFTAAV 238 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GGIGNLAGAVVG +LLGL+EAIG+GY+G LTGG+LGSHY DIFAF+ L+++LTLRP GL Sbjct: 239 LGGIGNLAGAVVGALLLGLLEAIGAGYLGDLTGGVLGSHYADIFAFMALVLVLTLRPQGL 298 Query: 301 LGERVADRA 309 LGER ADRA Sbjct: 299 LGERTADRA 307 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: 336 Number of extensions: 7 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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