Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo3_N2E3:AO353_16280 (223 letters) >FitnessBrowser__psRCH2:GFF3102 Length = 365 Score = 138 bits (348), Expect = 1e-37 Identities = 79/216 (36%), Positives = 125/216 (57%), Gaps = 8/216 (3%) Query: 9 VQAVP-GMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPL 67 +Q VP W G+++T+ + +G+ G + LG LLAL R S + + ++ ++R +PL Sbjct: 147 LQTVPTSQWGGLMLTVVIAAVGIAGALPLGILLALGRRSDMPAIRVLCVTFIEFWRGVPL 206 Query: 68 LLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMG 127 + V+ + +P L E + ++ + FEAAY E+VR G+Q+IPKGQ Sbjct: 207 ITVLFMSSVMLPLFLP----EGMNLDKLLRAMLMVVFFEAAYIAEVVRGGLQAIPKGQYE 262 Query: 128 AAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNA-TRASG 186 AA A+G+GY + L+ILPQA + + P ++ I LF+DTSLV +GL DFLN+ RA+ Sbjct: 263 AAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDFLNSIKRATA 322 Query: 187 D--IIGRANEFLIIAGLVYFTISFAASRLVKRLQKR 220 D +G + E + A LVY+ F SR RL+++ Sbjct: 323 DPAWLGMSTEGYVFAALVYWMFCFGMSRYSMRLERK 358 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: 224 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: 223 Length of database: 365 Length adjustment: 26 Effective length of query: 197 Effective length of database: 339 Effective search space: 66783 Effective search space used: 66783 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: 47 (22.7 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