Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate SMa0493 SMa0493 ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >FitnessBrowser__Smeli:SMa0493 Length = 232 Score = 151 bits (381), Expect = 1e-41 Identities = 81/208 (38%), Positives = 127/208 (61%), Gaps = 9/208 (4%) Query: 23 SMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILLIFYGGQDLLNRVAPM 82 S++L ++ GL+G + +LS R +G+ Y+ RG P++++ILL+++G L +A + Sbjct: 25 SLILMVIFGLLGASAKLSSNRLANAVGNAYTVFFRGTPEILVILLLYFGSAVSLTTIARV 84 Query: 83 FGYD-DYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGMAYGMSSFQVFFR 141 F ++D+ P AG + + G+Y +ETFRGAF + G EA A GM+ Q FF Sbjct: 85 FDPSVAFVDIPPFWAGSIAIALVVGSYATETFRGAFNGVKSGSIEAARALGMNGLQTFFY 144 Query: 142 VLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADATREPFTFFLAVAAM 201 + +P+M R+A+P F N+ L L K TALIS++GL + +F AKQAA T +PFT ++ V + Sbjct: 145 IRIPEMWRIALPPFGNHMLSLIKDTALISIIGLNETLFVAKQAASTTGKPFTMYIVVGLI 204 Query: 202 YL-----VITSVSL---LALRHLEKRYS 221 YL + SV L LA RH+++R S Sbjct: 205 YLGFSTAITISVLLLEALANRHIQRRPS 232 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: 142 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: 232 Length adjustment: 23 Effective length of query: 206 Effective length of database: 209 Effective search space: 43054 Effective search space used: 43054 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