Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 100 bits (250), Expect = 8e-26 Identities = 71/211 (33%), Positives = 112/211 (53%), Gaps = 19/211 (9%) Query: 146 LLVALPILSAILLPG-GW--FGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRR 202 +++AL + S + P GW FG + P+ GL TL+L+ +G LG LAL R Sbjct: 53 VVIALVLYSVLTNPRWGWGVFGEYFFSEPVLVGLGRTLLLTALGALFGFTLGTALALARV 112 Query: 203 SNMPVIKMLCTVFIEVIRGVPLITVLFM----------ASVMLPLF------LPQGVTFD 246 S P++ L FI + R +P+I +L + SV LP P Sbjct: 113 SRSPLLAGLSWTFIWIFRSIPVIVLLLIINNLGYLYETVSVGLPFTDWTFFSYPTTQLIS 172 Query: 247 KFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVI 306 F+ ALIG++L +A+ +E+VRGG+ ++ +GQ E A +LGL ++ IVLPQA++ ++ Sbjct: 173 PFVAALIGLTLNQAAFASEIVRGGILSVDQGQLEAAAALGLPRRRQAFRIVLPQAMRSIL 232 Query: 307 PGIVNTFIGLFKDTSLVSIIGMFDLLGIVRL 337 P N IGL K TS V I+ + +L +++ Sbjct: 233 PAGFNDIIGLAKGTSNVYILALPELFYTIQI 263 Lambda K H 0.329 0.144 0.454 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: 532 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 604 Length adjustment: 34 Effective length of query: 350 Effective length of database: 570 Effective search space: 199500 Effective search space used: 199500 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: 51 (24.3 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