Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_004326833.1 C665_RS18760 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >NCBI__GCF_000310185.1:WP_004326833.1 Length = 216 Score = 99.8 bits (247), Expect = 4e-26 Identities = 67/216 (31%), Positives = 111/216 (51%), Gaps = 14/216 (6%) Query: 9 ILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVLILLI 68 + +G+ +TLQL L ++ LA+ LGL +R+S R ++ + Y ++RG P ++ +L I Sbjct: 11 LAEGSLVTLQLFLITLLLAVPLGLALALVRISRFRVASQAVNAYIWLMRGTPLMLQMLFI 70 Query: 69 FYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAG 128 +Y P +G I L A I + AY +E FR +I +GQ E Sbjct: 71 YYALP-----FVPGIG----IRLPDFPAAIVAFALNYAAYFAEIFRAGIQSIDRGQYEGA 121 Query: 129 AAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADAT 188 G S Q R+++PQ+++ +P +N + L K T+LI V+ L D++ + A Sbjct: 122 KVLGFSYGQTMRRIVLPQVVKRILPPMSNETITLVKDTSLIYVLALNDLL---RAARGIV 178 Query: 189 REPFTF--FLAVAAMYLVITSVSLLALRHLEKRYSV 222 + FT F+ AA YL++T V + LEKR++V Sbjct: 179 QRDFTITPFIVAAAFYLIMTLVLTWLFQRLEKRHAV 214 Lambda K H 0.329 0.144 0.421 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: 148 Number of extensions: 8 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: 229 Length of database: 216 Length adjustment: 22 Effective length of query: 207 Effective length of database: 194 Effective search space: 40158 Effective search space used: 40158 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: 45 (21.9 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