Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_084055506.1 B9A12_RS00040 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_900176285.1:WP_084055506.1 Length = 287 Score = 177 bits (450), Expect = 2e-49 Identities = 101/286 (35%), Positives = 157/286 (54%), Gaps = 2/286 (0%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 M+L L+QL+NG+ +GS+YAL+ LG +VYGI+++++ AH +Y +GA++G L + Sbjct: 1 MHLFLEQLLNGVAIGSIYALVTLGLALVYGILRILHVAHAAVYTVGAYLG-LLFFKMSGS 59 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRA 120 V A+ A+LGV IE L Y PL LI +I + LE + G Sbjct: 60 LLVGCAGAIAGCAVLGVAIERLIYFPLLKYPPYVPLIASIAILLALEEVCRLVAGPYILT 119 Query: 121 FPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQL 180 FP ++ + + + + IL I+ ++ L + +T+ G AMRAVS D A Sbjct: 120 FPAQLRFPALHVLGVDVPSSVTGILCITAAILAFLWFLTTRTETGLAMRAVSQDLAIADA 179 Query: 181 MGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPG 240 MGIN + ISFTFA+GSA+A AGVL+ +YYN + MG P K+ V+GG+G +PG Sbjct: 180 MGINSHAVISFTFAVGSAIAAVAGVLVGIYYNQVYSTMGSVPAYKTLAIIVVGGLGSVPG 239 Query: 241 AALGGFVIGLLETFATAFGMSDF-RDAIVYGILLLILIVRPAGILG 285 A ++G+ ET + RDA+ + ++ +L+ R G+ G Sbjct: 240 AVAASLLLGIAETLLIGYAHIPLPRDALAFLAMIAVLMWRSEGLFG 285 Lambda K H 0.330 0.146 0.407 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: 206 Number of extensions: 14 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: 292 Length of database: 287 Length adjustment: 26 Effective length of query: 266 Effective length of database: 261 Effective search space: 69426 Effective search space used: 69426 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: 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