Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 102 bits (255), Expect = 1e-26 Identities = 69/219 (31%), Positives = 120/219 (54%), Gaps = 10/219 (4%) Query: 12 VPQLLAGALV-TVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLV 70 +P LL L T+ ++ S +LG ++G+++ + ++ R + + Y RG P +V Sbjct: 355 LPDLLKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWP-ARIYTDIFRGLPAVV 413 Query: 71 QLFILFFGLPQFGILLPA---FVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIG 127 + ++ G+ L + G + L + + AY+ E+ R IQS+D GQ+EA+R+IG Sbjct: 414 VILVVGLGIGPVVKNLTGNNPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEASRAIG 473 Query: 128 MSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTI----HDLMHEGQKIISVS 183 S +MR VV+PQ V R++P L N+FI+LIK+S+LV L + +L G+ ++ Sbjct: 474 FSYRQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRD-LNAQ 532 Query: 184 YRSLEVYLAIAVVYFILTGATTLVLRRIELRLRAGGMVQ 222 +L +A ++Y +LT T ++ I+ RLR G Q Sbjct: 533 TGNLSPLVAAGLIYLVLTIPLTHLVNYIDHRLRTGRPTQ 571 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: 264 Number of extensions: 13 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: 222 Length of database: 589 Length adjustment: 29 Effective length of query: 193 Effective length of database: 560 Effective search space: 108080 Effective search space used: 108080 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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