Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_054254746.1 BN2503_RS00885 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_05500 (242 letters) >NCBI__GCF_001298675.1:WP_054254746.1 Length = 217 Score = 131 bits (330), Expect = 9e-36 Identities = 84/221 (38%), Positives = 126/221 (57%), Gaps = 10/221 (4%) Query: 14 FSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGV 73 ++L GPL QG +T+KL ++L+L+V LGL+ A A+LSR+KLL Y L+RG Sbjct: 3 YALSLLGPL-GQGALVTLKLFVITLVLAVPLGLVLALARLSRLKLLSAGVNGYIWLMRGT 61 Query: 74 PDLVLMLLIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAV 133 P ++ ML I+++L F+ + + F A V Y AYF E FR I +V Sbjct: 62 PLMLQMLFIYFALP--------FVPVIGVRLPDFPAAVAAFALNYAAYFAEIFRAGIQSV 113 Query: 134 PRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKA 193 RGQ EAA G+ GQ R VV PQM+R LP + N + ++K T+L+ ++ L DL++A Sbjct: 114 DRGQYEAAKVLGMNYGQTMRRVVLPQMVRNILPPMSNETITLVKDTSLIYVLALNDLLRA 173 Query: 194 AQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYA 234 A+ + + F+V AA YL++T + + LE+RYA Sbjct: 174 ARGIVQRDFTTTPFIV-AAAFYLVMTLVLTWAFQRLEQRYA 213 Lambda K H 0.329 0.142 0.423 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: 172 Number of extensions: 12 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: 242 Length of database: 217 Length adjustment: 23 Effective length of query: 219 Effective length of database: 194 Effective search space: 42486 Effective search space used: 42486 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: 46 (22.3 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