Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate RR42_RS04400 RR42_RS04400 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_05500 (242 letters) >FitnessBrowser__Cup4G11:RR42_RS04400 Length = 219 Score = 139 bits (350), Expect = 5e-38 Identities = 78/218 (35%), Positives = 130/218 (59%), Gaps = 11/218 (5%) Query: 21 PLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGVPDLVLML 80 P+L+QG +TIK + LS++ ++LG + A +S + + A+ Y +++RG P LV + Sbjct: 12 PVLLQGMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSIMRGTPLLVQIF 71 Query: 81 LIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAVPRGQVEA 140 +++Y L I ++P AGV+TL GAY +E+ RGAIL +PRGQ A Sbjct: 72 VVYYGLPGI-----------GIALEPTPAGVLTLSLNVGAYLSESMRGAILGIPRGQWLA 120 Query: 141 ATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKS 200 A + GL +GQ R+V+ PQ +R A+P + N+ + ++K T+LVS+I + +L++ AQ+ + Sbjct: 121 AYSLGLTQGQALRYVIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELLRTAQEVIAA 180 Query: 201 TYQLFYFLVLAALIYLLITSASNFILRWLERRYAAGAR 238 TYQ + A IY ++++A + R LERR + R Sbjct: 181 TYQPLPLYLAVAAIYWMLSTALAHMQRLLERRLSLPGR 218 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: 151 Number of extensions: 5 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: 242 Length of database: 219 Length adjustment: 23 Effective length of query: 219 Effective length of database: 196 Effective search space: 42924 Effective search space used: 42924 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