Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_086508347.1 BZY95_RS02055 ABC transporter
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >NCBI__GCF_002151265.1:WP_086508347.1 Length = 233 Score = 239 bits (609), Expect = 4e-68 Identities = 124/226 (54%), Positives = 164/226 (72%), Gaps = 4/226 (1%) Query: 2 LKGYGAVILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPD 61 L GYG +L+G +TLQLA+ S++LA++LGL+ + ++S L + LY+TVIRG+PD Sbjct: 4 LHGYGPRLLEGAGVTLQLAVLSLILALILGLLTASAKMSRNWLLHKVATLYTTVIRGVPD 63 Query: 62 LVLILLIFYGGQDLLN----RVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAF 117 LVL+LL+F+GGQ LN + FG D YI+LN AAG+ T+GFIFGAY+ ETFRGAF Sbjct: 64 LVLMLLLFFGGQMALNVATDAIYDRFGVDWYINLNAFAAGVLTIGFIFGAYMGETFRGAF 123 Query: 118 MAIPKGQAEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDM 177 MA+ GQ EAG AYGMS + VF R+ PQM+R A+PG +NNW+VL K TAL+SV+GL DM Sbjct: 124 MAVEHGQIEAGKAYGMSPWLVFRRIRFPQMMRHALPGISNNWMVLLKTTALVSVIGLSDM 183 Query: 178 MFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVG 223 + A +A+ AT EPFTF + VA +YL+I SVS L+KRY+VG Sbjct: 184 VRVAAEASRATHEPFTFLIPVAVVYLLIASVSEWMFARLQKRYNVG 229 Lambda K H 0.329 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: 218 Number of extensions: 7 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: 229 Length of database: 233 Length adjustment: 23 Effective length of query: 206 Effective length of database: 210 Effective search space: 43260 Effective search space used: 43260 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 24 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