Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate AZOBR_RS23520 AZOBR_RS23520 ABC transporter permease
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__azobra:AZOBR_RS23520 Length = 220 Score = 110 bits (276), Expect = 2e-29 Identities = 73/222 (32%), Positives = 117/222 (52%), Gaps = 12/222 (5%) Query: 3 EFLNLHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVP-ATLYTTLI 61 +F + G P L +G +T+++ A LS LGL+ +L+ A+ + A+ Y I Sbjct: 4 DFAPVWGGLPELLKGTVVTIEVTAAAFLLSAVLGLLVGIIRLNPARRVLYGIASAYVAFI 63 Query: 62 RSVPDLVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAI 121 R P LV + L+F+ L FG + GVI LG G+Y +E RGAI Sbjct: 64 RGTPLLVQLFLLFFGLPQ--------FG---ILLPAMLCGVIGLGIYSGSYVSEVVRGAI 112 Query: 122 LSVPVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDL 181 S+ GQ+EAA + G+S + V+ PQ R LP LGN + L+K++ALVS++ + D+ Sbjct: 113 QSIDRGQMEAARSLGMSYREAMWEVVLPQAFRRMLPPLGNETIALIKNSALVSLLTIDDV 172 Query: 182 VKAAQNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERR 223 ++ Q T+ L I L+Y V+T + +L+++E+R Sbjct: 173 MREGQRIISTSFRALEVYIAVALIYFVLTNAATWILRQIEKR 214 Lambda K H 0.327 0.141 0.428 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: 128 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: 233 Length of database: 220 Length adjustment: 22 Effective length of query: 211 Effective length of database: 198 Effective search space: 41778 Effective search space used: 41778 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: 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