Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate 206098 DVU0674 ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >MicrobesOnline__882:206098 Length = 271 Score = 112 bits (281), Expect = 5e-30 Identities = 69/212 (32%), Positives = 114/212 (53%), Gaps = 13/212 (6%) Query: 8 VILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILL 67 ++L G+ +TLQ+A S+VLA++L + VALRLS +R + LY +R P LV + + Sbjct: 68 LLLQGLGVTLQVAAGSLVLALLLAAVAVALRLSCLRTGRLVARLYVESVRNTPLLVQLFV 127 Query: 68 IFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127 ++ +AP+FG L +A+ + LG GAY++E R A+P+GQ EA Sbjct: 128 TYFA-------IAPVFG------LGRMASAVMALGVFEGAYMAEILRAGIAAVPQGQWEA 174 Query: 128 GMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187 + GM + +V++PQ +R A+P T + L K ++L S + + ++ +A+ Sbjct: 175 SRSLGMDEPGTYVQVILPQALRRALPPLTGQAVSLVKDSSLASAIAIHELTMQAQTIIAE 234 Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 T F +L AA+YL +T R LE+R Sbjct: 235 TFLTFEVWLLTAAIYLCVTLSLSAVARLLERR 266 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: 154 Number of extensions: 9 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: 271 Length adjustment: 24 Effective length of query: 205 Effective length of database: 247 Effective search space: 50635 Effective search space used: 50635 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