Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_109969949.1 DK846_RS15745 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >NCBI__GCF_003173355.1:WP_109969949.1 Length = 218 Score = 119 bits (297), Expect = 6e-32 Identities = 62/199 (31%), Positives = 112/199 (56%), Gaps = 9/199 (4%) Query: 13 PLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQLF 72 P ++ GL+ TL L+A++ G + + RV +V+ YT +G P+L+ LF Sbjct: 13 PAFWNGLLVTLSLIAVTAPIGFALGIIIACGRVYGGKVVSKIFQGYTIFFKGCPLLLLLF 72 Query: 73 LIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAK 132 ++Y+GL + F+ + + F + SAY +E + G++ + G+I AAK Sbjct: 73 ILYFGLPPYGITLSPFV---------ASVIGFILCNSAYNSEYVRGAILSVKEGQITAAK 123 Query: 133 AMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYY 192 A+GM+R + + ++LP ALRRA+P SNE I +++ +SLA ++T+I++TGA + + +Y+ Sbjct: 124 ALGMTRNQAIRFVVLPQALRRAIPGISNEFIYLIKYSSLAYMITVIELTGAGKLIATKYF 183 Query: 193 LPFEAYITAGVFYLCMTFI 211 E + + YL + I Sbjct: 184 AYNETFFALAIVYLALVTI 202 Lambda K H 0.329 0.139 0.427 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: 123 Number of extensions: 2 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: 232 Length of database: 218 Length adjustment: 22 Effective length of query: 210 Effective length of database: 196 Effective search space: 41160 Effective search space used: 41160 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