Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 94.0 bits (232), Expect = 4e-24 Identities = 57/167 (34%), Positives = 92/167 (55%), Gaps = 9/167 (5%) Query: 12 GVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILLIFYG 71 G+ LTL AL SMV ++ LG++ R S + + WL Y + RG+P L+ ++F+G Sbjct: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLP---LVTILFFG 246 Query: 72 GQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGMAY 131 +V D ++ + I L AYL+ET RG AIP+GQ EA A Sbjct: 247 ------QVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAAL 300 Query: 132 GMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMM 178 G++ FQ + +++PQ +R++IP +L L + T L+S+VGL +++ Sbjct: 301 GLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELL 347 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: 319 Number of extensions: 27 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: 396 Length adjustment: 27 Effective length of query: 202 Effective length of database: 369 Effective search space: 74538 Effective search space used: 74538 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: 48 (23.1 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