Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate AO356_23510 AO356_23510 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_05500 (242 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23510 Length = 229 Score = 219 bits (559), Expect = 3e-62 Identities = 112/220 (50%), Positives = 158/220 (71%), Gaps = 2/220 (0%) Query: 16 LQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGVPD 75 L+G+G L+ QG W+T++++ + ++++LGLLGA AKLS + LR+ A LYTTL+R VPD Sbjct: 3 LEGYGYLIFQGAWLTVQVATWAACVALVLGLLGALAKLSPLAPLRLVATLYTTLVRSVPD 62 Query: 76 LVLMLLIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAVPR 135 LVLMLLI+YS Q L + E ++++P+G + TLGFIYGAY ETFRGA A+ Sbjct: 63 LVLMLLIYYSAQIGLNQVAEAFGRESLQLNPYGTAIGTLGFIYGAYCAETFRGAFQAIAF 122 Query: 136 GQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQ 195 GQ+EAA AYG+ Q R + PQMMRFALPGIGN W V+LK+ L+S++GL D+V+ A+ Sbjct: 123 GQLEAARAYGMSHWQVLRRIRLPQMMRFALPGIGNIWQVLLKSAGLISLLGLNDMVQVAK 182 Query: 196 DAGKST-YQLFYFLVLAALIYLLITSASNFILRWLERRYA 234 AG +T Q+F++LV+AA I+L S+ +L+ LERRY+ Sbjct: 183 QAGNATSRQMFFYLVIAA-IFLAFAILSSLVLKHLERRYS 221 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: 192 Number of extensions: 8 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: 229 Length adjustment: 23 Effective length of query: 219 Effective length of database: 206 Effective search space: 45114 Effective search space used: 45114 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