Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate AO356_27115 AO356_27115 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_2959 (242 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27115 Length = 242 Score = 400 bits (1029), Expect = e-117 Identities = 203/242 (83%), Positives = 223/242 (92%) Query: 1 MFEQLLQNLGLSAFSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLR 60 MFE LL LGLSAFSLQGFGPLL++G WMT+KLS +L LSVLLGL+GASAKLSS+KLLR Sbjct: 1 MFETLLGALGLSAFSLQGFGPLLLEGAWMTVKLSLSALALSVLLGLIGASAKLSSLKLLR 60 Query: 61 IPAQLYTTLIRGVPDLVLMLLIFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGA 120 +PAQLYTTLIRGVPDLVLMLLIFYSLQTWLT +T + WEYIEI+PF AG+ITLGFIYGA Sbjct: 61 LPAQLYTTLIRGVPDLVLMLLIFYSLQTWLTVITVALGWEYIEINPFVAGIITLGFIYGA 120 Query: 121 YFTETFRGAILSVPRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATA 180 YFTETFRGA+L+VPRGQVEAATAYGL R QRFRFVVFPQMMRFALPG+GNNWMV+LKATA Sbjct: 121 YFTETFRGAMLAVPRGQVEAATAYGLSRAQRFRFVVFPQMMRFALPGLGNNWMVILKATA 180 Query: 181 LVSIIGLADLVKAAQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYAAGAREA 240 LVSIIGLADLVKAAQDAGKSTYQLF+FLVLAAL YL+ITS SNF+LR LE+ YAAG+REA Sbjct: 181 LVSIIGLADLVKAAQDAGKSTYQLFFFLVLAALTYLIITSISNFVLRCLEKHYAAGSREA 240 Query: 241 VR 242 R Sbjct: 241 AR 242 Lambda K H 0.329 0.142 0.418 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: 273 Number of extensions: 7 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: 242 Length of database: 242 Length adjustment: 23 Effective length of query: 219 Effective length of database: 219 Effective search space: 47961 Effective search space used: 47961 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 17 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