Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate RR42_RS04400 RR42_RS04400 ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772 (223 letters) >FitnessBrowser__Cup4G11:RR42_RS04400 Length = 219 Score = 117 bits (293), Expect = 2e-31 Identities = 73/219 (33%), Positives = 121/219 (55%), Gaps = 13/219 (5%) Query: 8 IIPSLPGLWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPL 67 + SLP L GM++T+K + +I G++LGT++ALM +SH V +A AYV+ R PL Sbjct: 7 VATSLPVLLQGMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSIMRGTPL 66 Query: 68 LLVITWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMG 127 L+ I Y +P + I E TP G ++ + AY E +R + IP+GQ Sbjct: 67 LVQIFVVYYGLPGI--GIALEPTPAG-----VLTLSLNVGAYLSESMRGAILGIPRGQWL 119 Query: 128 AAQALGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGD 187 AA +LG++ GQ +R +I PQA R P L I L +DTSLV + + + L R + + Sbjct: 120 AAYSLGLTQGQALRYVIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELL---RTAQE 176 Query: 188 IIGRSNEFL---IFAGLVYFIISFAASQLVKRLQKRFAV 223 +I + + L + +Y+++S A + + + L++R ++ Sbjct: 177 VIAATYQPLPLYLAVAAIYWMLSTALAHMQRLLERRLSL 215 Lambda K H 0.332 0.144 0.428 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: 125 Number of extensions: 4 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: 223 Length of database: 219 Length adjustment: 22 Effective length of query: 201 Effective length of database: 197 Effective search space: 39597 Effective search space used: 39597 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 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