Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_012404721.1 BPHY_RS27410 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >NCBI__GCF_000020045.1:WP_012404721.1 Length = 219 Score = 119 bits (298), Expect = 5e-32 Identities = 73/212 (34%), Positives = 119/212 (56%), Gaps = 12/212 (5%) Query: 8 VILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVLILL 67 V+L GA +TL+ AL+S L +++G I + +S +A + Y +++RG P LV I + Sbjct: 13 VLLLGAMVTLKFALASAVLGLLVGFIVAIMGISGQPIIAGIARAYVSLMRGTPLLVQIFV 72 Query: 68 IFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127 ++YG DL I L+P AGI L GAYLSE+ RGA + I +GQ A Sbjct: 73 VYYGLPDL------------GISLDPTSAGILALTANAGAYLSESMRGAILGISQGQWGA 120 Query: 128 GAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187 + G++ Q V+ PQ +R+A+P N + L K T+L+SV+ + +M+ A++ + Sbjct: 121 AHSLGLTHMQTLRYVICPQALRMAVPSLGNTLISLIKDTSLVSVITVTEMLRAAQEVIAS 180 Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 T +P +LA AA+Y ++++ RH+E R Sbjct: 181 TFQPLPLYLAAAAIYWLLSTGMSWVQRHVEVR 212 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: 153 Number of extensions: 14 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: 219 Length adjustment: 22 Effective length of query: 207 Effective length of database: 197 Effective search space: 40779 Effective search space used: 40779 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 Apr 09 2024. 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