Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate Dsui_0636 Dsui_0636 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >FitnessBrowser__PS:Dsui_0636 Length = 245 Score = 109 bits (272), Expect = 5e-29 Identities = 68/218 (31%), Positives = 117/218 (53%), Gaps = 8/218 (3%) Query: 9 ILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILLI 68 + G+ T+ L+LS+ V+A+V+G I LR P RWL+ +Y R +P LV + Sbjct: 25 LFTGLQWTVALSLSAWVIALVVGSIVGVLRTVPNRWLSGFAAVYVECFRNVPLLVQLFSW 84 Query: 69 FYGGQDLLNRVAPMFGYDDYIDLNPLA----AGIGTLGFIFGAYLSETFRGAFMAIPKGQ 124 ++ +LL P G + Y +PL A + LG A ++E R ++P+GQ Sbjct: 85 YFVLPELL---PPALG-NAYKQSDPLLQQFLAAMLCLGLFTAARVAEQVRAGIESLPRGQ 140 Query: 125 AEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQA 184 AG+A G + QV+ VL+P R+ +P T+ +L + K +A+ + +GL ++ +A+Q Sbjct: 141 RNAGLAMGFTLAQVYRHVLLPMAFRIIVPPLTSEFLNIFKNSAVATTIGLIELSRQAQQL 200 Query: 185 ADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSV 222 D T +P+ F+AV +Y+ I + +R LE++ V Sbjct: 201 VDYTAQPYEAFIAVTLLYVCINVTVMFLMRRLEEKVRV 238 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: 150 Number of extensions: 6 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: 245 Length adjustment: 23 Effective length of query: 206 Effective length of database: 222 Effective search space: 45732 Effective search space used: 45732 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 17 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