Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >NCBI__GCF_003217355.1:WP_110804905.1 Length = 262 Score = 95.5 bits (236), Expect = 9e-25 Identities = 65/215 (30%), Positives = 109/215 (50%), Gaps = 6/215 (2%) Query: 7 AVILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAW--LGDLYSTVIRGIPDLVL 64 A + G+ +T+ + L + A+VLGL+ LS R L W L Y+ VIRG+P +V+ Sbjct: 38 ATLSKGIGITVFVTLFAFAGALVLGLVLAVASLS--RHLIWRQLARFYTEVIRGVPIIVM 95 Query: 65 ILLIFYGGQDLLNRVAPMFGYDDYI--DLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPK 122 +L + + + G + D LA + L + A+L+E FR +++ + Sbjct: 96 LLYVAFALVPAVVAGWNALGLPEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVER 155 Query: 123 GQAEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAK 182 GQ EA A G++ + F ++ PQ R +P N+++ + K ++L+SV+G+ D+ K Sbjct: 156 GQIEAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGK 215 Query: 183 QAADATREPFTFFLAVAAMYLVITSVSLLALRHLE 217 A F + VA +YL +T LALR LE Sbjct: 216 VTAAGNFRYFETYNVVALIYLAMTVTLSLALRKLE 250 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: 159 Number of extensions: 8 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: 262 Length adjustment: 24 Effective length of query: 205 Effective length of database: 238 Effective search space: 48790 Effective search space used: 48790 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