Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate WP_081718345.1 N177_RS02595 ABC transporter permease
Query= reanno::WCS417:GFF4243 (232 letters) >NCBI__GCF_000496075.1:WP_081718345.1 Length = 248 Score = 174 bits (442), Expect = 1e-48 Identities = 89/213 (41%), Positives = 133/213 (62%), Gaps = 2/213 (0%) Query: 16 LGGLLTTLKLLAISLFFGLLAALPLGLMRVSKQPIVNGAAWLYTYVIRGTPMLVQLFLIY 75 L G TT++L+ +SL G +LP+ R+S P++ A+ Y Y RGTP+L Q FL+Y Sbjct: 32 LSGFWTTIELVTLSLLIGAAISLPVAAGRLSPNPVIGALAYGYVYFFRGTPLLAQTFLVY 91 Query: 76 YGLAQFEAVRESF-LWPLLSSATFCACLAFAINTSAYTAEIIAGSLKATPNGEIEAAKAM 134 YG F A ++ LW A FCA F++NTSAY AEI+AG+++ P +IEA +A+ Sbjct: 92 YGAGSFRAELDAVGLWTFFRDAWFCAVFTFSLNTSAYQAEILAGAIRTVPRSQIEAGQAL 151 Query: 135 GMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQFYLP 194 G+SRY + RI+LP AL AL Y NEV++M++ +++ASI+T+ D+ G R ++ + Sbjct: 152 GLSRYVIATRIVLPQALVVALRPYGNEVVLMIKGSAIASIITIYDLMGETRRAFSRSF-D 210 Query: 195 FEAYITAGVFYLCLTFILVRLFKLAERRWLSYL 227 F+ YI A + YL L L RL+ + ERR +L Sbjct: 211 FQTYIWAAILYLVLVETLRRLWDVMERRLTRHL 243 Lambda K H 0.329 0.140 0.422 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: 7 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: 232 Length of database: 248 Length adjustment: 23 Effective length of query: 209 Effective length of database: 225 Effective search space: 47025 Effective search space used: 47025 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