Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_022528091.1 L248_RS00665 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >NCBI__GCF_000469325.1:WP_022528091.1 Length = 215 Score = 98.6 bits (244), Expect = 8e-26 Identities = 68/214 (31%), Positives = 114/214 (53%), Gaps = 15/214 (7%) Query: 9 ILDGVWLTLQLALSSMVLAIVLG-LIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILL 67 +L G +TL + L ++VL+I LG L+ V LR S + L WL D Y ++RG P L+ ++ Sbjct: 13 LLSGTKITLIIFLGTLVLSIPLGILVSVGLR-SRFKPLVWLLDGYVWLMRGTPLLLQLIF 71 Query: 68 IFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127 IFYG P+ I + ++A + AY +E FRG AIP+GQ +A Sbjct: 72 IFYG--------LPVIA----IYFDRMSAVFLAFVLNYAAYFAEIFRGGLQAIPQGQYDA 119 Query: 128 GMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187 ++ ++ F +++PQ+++ IP N + L K ++L+ V+G+ D++ +A A A Sbjct: 120 AKVLKLTPWETFRLIVLPQVVKNVIPAVGNEVINLIKDSSLVYVLGIGDLL-RAGNIASA 178 Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKRYS 221 + V +YL +T++ LR LEK Y+ Sbjct: 179 RDVTLVPLVLVGIVYLTLTALLTWGLRSLEKHYA 212 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: 157 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: 215 Length adjustment: 22 Effective length of query: 207 Effective length of database: 193 Effective search space: 39951 Effective search space used: 39951 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