Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate WP_090438604.1 BLS63_RS01120 ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >NCBI__GCF_900100495.1:WP_090438604.1 Length = 229 Score = 85.1 bits (209), Expect = 2e-21 Identities = 63/217 (29%), Positives = 115/217 (52%), Gaps = 17/217 (7%) Query: 170 YLPWPQTPGWLVV-ILAIALV--LFVSWLAQRQRSPRDWRWLY-----------GAIAVV 215 +LP WL + ++AIA++ L ++ RS R W WL G +V Sbjct: 9 WLPRIAEGAWLTLELVAIAVIAGLILAIPLGIARSSRQW-WLRSLPYAYIFFFRGTPLLV 67 Query: 216 TVLMLLTQLSWPQQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQ 275 + ++ L+ ++ G + LR + ++ L +T A+I EI+RG I ++P G+ Sbjct: 68 QLFLVYYGLAQFDAVRQGPLWPYLRDP--YWCAIITLTLHTAAYIAEILRGAIQAIPPGE 125 Query: 276 WEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTT 335 EAA ALG++R+Q L I++P+A R+ +P+ +++ + K S+LA + +L ++T Sbjct: 126 IEAARALGMSRAQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGMSRTI 185 Query: 336 LNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRLQ 372 + +T +PVE+F + YL V+ G L++RL+ Sbjct: 186 IARTYQPVEIFFAAGVFYLLAAYVLVQGFRLLERRLR 222 Lambda K H 0.326 0.140 0.445 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: 244 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 229 Length adjustment: 26 Effective length of query: 351 Effective length of database: 203 Effective search space: 71253 Effective search space used: 71253 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 (21.7 bits) S2: 48 (23.1 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