Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate Ac3H11_4900 Putative amino acid ABC transporter, permease protein
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4900 Length = 217 Score = 124 bits (312), Expect = 1e-33 Identities = 77/221 (34%), Positives = 120/221 (54%), Gaps = 9/221 (4%) Query: 8 LFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPL 67 L+D ++ LL A T+ L + I GGL+ L+++ +R+S +R AY+ VF+G+PL Sbjct: 6 LWDILRNLLLAARWTVSLSLIAFIGGGLVGLLLLVLRLSKVRGVDRAVGAYVQVFQGTPL 65 Query: 68 LIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQ 127 L+Q+FL Y+G+ FG+ P+ A ++L L T+ Y EI RG + ++P GQ Sbjct: 66 LMQLFLAYFGIALFGI---------KTSPWTAAAVALTLYTSAYLTEIWRGCVASIPKGQ 116 Query: 128 IEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQI 187 EA S+ + LR V+ P ALR +P V ++K TALAS++ E+T I Sbjct: 117 WEAAQSLAFNFGEQLRHVVLPQALRIAVPPTVGFLVQVIKGTALASVIGFVELTKAGSMI 176 Query: 188 IQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLR 228 TY+ V+ C AL+Y L F + + LE +L + R Sbjct: 177 SNATYKPFLVYACVALLYFVLCFPVSLVAQSLERKLHGNRR 217 Lambda K H 0.331 0.143 0.431 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: 125 Number of extensions: 7 Number of successful extensions: 3 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: 250 Length of database: 217 Length adjustment: 23 Effective length of query: 227 Effective length of database: 194 Effective search space: 44038 Effective search space used: 44038 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: 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