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_041275796.1 DESRU_RS13875 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_000215085.1:WP_041275796.1 Length = 297 Score = 285 bits (730), Expect = 7e-82 Identities = 147/293 (50%), Positives = 213/293 (72%), Gaps = 3/293 (1%) Query: 3 LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62 + LQ L NG+ LGS+YAL+A+GYTMVYGI++LINFAH D+ M+ A++ ++ I F + ++ Sbjct: 5 VFLQNLANGISLGSLYALIAIGYTMVYGILRLINFAHADLLMVAAYVAFYGILLFSLPWW 64 Query: 63 VALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFP 122 +A +A++ TA+LG+ IE +AYRPLR + RI+VLI+AIGVSFLLE + +GA + FP Sbjct: 65 LAFALAVIFTALLGMSIEKVAYRPLRDAPRISVLISAIGVSFLLENLGIVAIGARPKTFP 124 Query: 123 QAIQTV-RYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLM 181 + V ++G IS ++ ++I ++++L++ + +V KTK G AMRAVS D +AA LM Sbjct: 125 RPESMVWNINVGDISFLSLTVIIPVVTILLLVAVTYLVNKTKTGTAMRAVSRDFEAASLM 184 Query: 182 GINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGA 241 I+VN+ IS TF +GS LAG G++ +L Y ++PLMGV PGLK F+AAV+GGIG IPGA Sbjct: 185 AIDVNKVISTTFIVGSGLAGIGGIMWSLQYPQIDPLMGVFPGLKCFIAAVMGGIGSIPGA 244 Query: 242 ALGGFVIGLLETFATAF--GMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292 LGGF++G+ E F AF +S +RDA + +L+ IL+ +P GILG+NV EKV Sbjct: 245 MLGGFILGMGEVFLVAFMPELSGYRDAFAFVVLIFILLFKPTGILGENVVEKV 297 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: 257 Number of extensions: 11 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: 297 Length adjustment: 26 Effective length of query: 266 Effective length of database: 271 Effective search space: 72086 Effective search space used: 72086 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