Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate 5210737 Shew_3165 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >FitnessBrowser__PV4:5210737 Length = 226 Score = 101 bits (251), Expect = 1e-26 Identities = 65/212 (30%), Positives = 107/212 (50%), Gaps = 13/212 (6%) Query: 8 VILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILL 67 +IL+G+ +TL + L +M+L +LG+ +++S +L W +LY VIRG P +V +++ Sbjct: 23 LILNGLKVTLIVTLFAMILGAILGVATTLMKMSSRWYLRWPANLYVGVIRGTPVVVQLVI 82 Query: 68 IFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127 +++ V + D++ ++A I G GAY+SE R A+ KGQ EA Sbjct: 83 LYF-------IVLATW------DVDKVSAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEA 129 Query: 128 GMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187 + G+S V++PQ I+ +P N ++VL K TA+I +G D+M + Sbjct: 130 ARSLGLSQAVTMKEVILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRSGEIIRSR 189 Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 T E A +YL +T L EKR Sbjct: 190 TFEDSVPLFTCALIYLALTYSFTFMLSKFEKR 221 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: 127 Number of extensions: 5 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: 226 Length adjustment: 22 Effective length of query: 207 Effective length of database: 204 Effective search space: 42228 Effective search space used: 42228 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