Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate H281DRAFT_02563 H281DRAFT_02563 amino acid ABC transporter membrane protein, PAAT family
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Burk376:H281DRAFT_02563 Length = 265 Score = 106 bits (264), Expect = 9e-28 Identities = 67/216 (31%), Positives = 116/216 (53%), Gaps = 20/216 (9%) Query: 175 GLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLF----- 229 GL+ TL+LS V A+ + G+ LAL S+ + VF++V RG+P V+ Sbjct: 25 GLVNTLILSVVSTALGIVAGMALALCAVSHTRWLTWPVRVFVDVFRGLPAALVILVVGQG 84 Query: 230 MASVMLPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSF 289 +A V L LF P + + A++ ++L +SAY+AE+ R G+Q++ +GQ +LG+++ Sbjct: 85 LAPVGLSLFGP-----NPYPLAIVALALVSSAYIAEIFRSGIQSVGRGQMSACQALGMTY 139 Query: 290 WQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMF----DLLGIVRLNFSDTNWA 345 W M +++PQ ++ ++P + N FI + KD+SLV +G+ DL I N A Sbjct: 140 WSGMRHVIVPQGVRRILPALANQFISIVKDSSLVYFLGLLTSQRDLFTI------GQNAA 193 Query: 346 TAVTPLTGLIFAGFVFWLFCFGMSRYSGFMERLLDR 381 L+ L+ AG V+ L ++ ++R +R Sbjct: 194 VNTANLSPLVAAGAVYLLITVPLTHTINHLDRWTNR 229 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: 257 Number of extensions: 11 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: 384 Length of database: 265 Length adjustment: 27 Effective length of query: 357 Effective length of database: 238 Effective search space: 84966 Effective search space used: 84966 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