Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate Ac3H11_2554 Amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_16280 (223 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2554 Length = 222 Score = 108 bits (269), Expect = 1e-28 Identities = 65/221 (29%), Positives = 122/221 (55%), Gaps = 8/221 (3%) Query: 1 MDLDFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSK-LLSNIAGAYV 59 M+LDFS V VP + G ++T+++T ++ G ++G L+ + RL+ + ++ + AYV Sbjct: 1 MELDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYV 60 Query: 60 NYFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQ 119 R PLL+ + + +P + AF ++ ++ AY E+VR +Q Sbjct: 61 AAIRGTPLLVQLFILFFGLPQF-------GILLPAFVCGVIGLGIYSGAYVSEVVRGAIQ 113 Query: 120 SIPKGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFL 179 SI KGQM AA+++GM G MR ++LPQA +M P L + I L ++++LV + + D + Sbjct: 114 SIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLM 173 Query: 180 NATRASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQKR 220 + + + R+ E + +VYF ++ A + +++R++ R Sbjct: 174 HEGQKIISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELR 214 Lambda K H 0.331 0.143 0.425 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: 118 Number of extensions: 7 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: 223 Length of database: 222 Length adjustment: 22 Effective length of query: 201 Effective length of database: 200 Effective search space: 40200 Effective search space used: 40200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 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