Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate PP_4426 PP_4426 Amino acid ABC transporter, permease protein
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__Putida:PP_4426 Length = 218 Score = 141 bits (355), Expect = 1e-38 Identities = 67/204 (32%), Positives = 126/204 (61%), Gaps = 1/204 (0%) Query: 12 VPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQ 71 +P+L AL T+ +T + V+GL + IGR + + + + + + IR TPLL+Q Sbjct: 13 LPELFRAALNTIGVTLLGFAIAIVLGLFLAIGRRSARIWISWPI-GGVIEFIRSTPLLIQ 71 Query: 72 LFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSG 131 ++ L++ LP +G+ L A GV+G+G++ Y++EV R + ++ +GQ EA ++ MS Sbjct: 72 VYFLYYVLPNYGVSLTAMQVGVLGIGLHYACYLAEVYRSGLDAVPRGQWEAVTALNMSPS 131 Query: 132 LAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYL 191 LA R ++LPQA+ ++PP+GN +A++K++ ++S +T+ ++M + + I S ++R LE Sbjct: 132 LAYRNIILPQALRPILPPVGNYLVAMLKDTPVLSAITVVEIMQQAKNIGSETFRYLEPIT 191 Query: 192 AIAVVYFILTGATTLVLRRIELRL 215 + V + L+ ++RR+E RL Sbjct: 192 MVGVFFLALSIVLAYLVRRVEARL 215 Lambda K H 0.328 0.143 0.412 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: 129 Number of extensions: 5 Number of successful extensions: 1 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: 222 Length of database: 218 Length adjustment: 22 Effective length of query: 200 Effective length of database: 196 Effective search space: 39200 Effective search space used: 39200 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: 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