Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate HSERO_RS21245 HSERO_RS21245 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__HerbieS:HSERO_RS21245 Length = 218 Score = 110 bits (276), Expect = 3e-29 Identities = 65/208 (31%), Positives = 115/208 (55%), Gaps = 12/208 (5%) Query: 179 TLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLF 238 T+VLS V + LG+++ R S ++ + ++IE+ +G PL+ LF+ + LF Sbjct: 20 TIVLSLVTFVLGGALGLVILFMRTSRQNWLRQVARLYIELFQGTPLLMQLFLVFFGIALF 79 Query: 239 LPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVL 298 G+ +L A + + ++++Y+AE+ RG ++AIPKGQ+E + L + ++Q+M +IVL Sbjct: 80 ---GIEVPAWLAAGLALMCWSASYLAEIWRGCVEAIPKGQWEASSVLAMGYFQQMRYIVL 136 Query: 299 PQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDL--LGIVRLNFSDTNWATAVTPLTGLIF 356 PQAL++ I V + + K T++ SIIG +L G V N P T Sbjct: 137 PQALRIAIAPTVGFGVQIIKSTAVTSIIGFIELSKAGTVITN-------ATFRPFTVFAI 189 Query: 357 AGFVFWLFCFGMSRYSGFMERLLDRSQR 384 G +++ C+ +S+YS +ER + + R Sbjct: 190 VGAFYFVLCWPLSKYSQSLERKYNAAHR 217 Lambda K H 0.329 0.144 0.454 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: 253 Number of extensions: 16 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: 384 Length of database: 218 Length adjustment: 26 Effective length of query: 358 Effective length of database: 192 Effective search space: 68736 Effective search space used: 68736 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: 48 (23.1 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