Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_110205942.1 DNK54_RS05350 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_003194585.1:WP_110205942.1 Length = 332 Score = 138 bits (348), Expect = 2e-37 Identities = 101/331 (30%), Positives = 160/331 (48%), Gaps = 40/331 (12%) Query: 138 FGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGI 197 FG ++Y + A GLNI G GLL+ G AF AVG Y+ A+ + + +S W+ + L+G+ Sbjct: 15 FGTSAIVYCLAAIGLNIHFGYTGLLNFGQAAFMAVGGYTMAMFVTQWDVSLWLAM-LAGL 73 Query: 198 -FAALWGVILGFPVLRLRGDYLAIVTLAFGEIIR-----LVLINWTDVTKGTFGISSIPK 251 A+ ++LG P LRLR DYLAIVT+A EI+R + L + G S+ + Sbjct: 74 GLTAVLAILLGIPTLRLRADYLAIVTIAAAEIVRQVYGSIALKKYFGAQDGLTAFSADFR 133 Query: 252 A-TLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAW 310 A F P D + K + + + + + ++ALC L ++ L R P GR Sbjct: 134 ALNPFDGPVDLGIVSWGK-------NDAWVVLVGWFVVALCCLVVWL---LMRSPWGRIL 183 Query: 311 EALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVIL 370 +++REDE A RSLG N K+ + G M AG A + ++P F + Sbjct: 184 KSIREDEDAVRSLGKNVYYYKMQSLMLGGMIGALAGFVTALKSAAINPSFFATDVTFFAY 243 Query: 371 AIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIF-------GPDFTP--------- 414 ++++GG + G + AI+ ++FL L F G P Sbjct: 244 TVLLIGGAARVLGPVVGAII------FWFLLTFLDLFFSAATDDVGSVLIPSSIMTNQQA 297 Query: 415 ELYRMLIFGLAMVVVMLFKPRGFVGSREPTA 445 L R ++ GLA++++M+F+P+G G R A Sbjct: 298 SLVRFIVMGLALMLLMIFRPQGIFGDRRELA 328 Lambda K H 0.330 0.145 0.432 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: 428 Number of extensions: 23 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: 463 Length of database: 332 Length adjustment: 31 Effective length of query: 432 Effective length of database: 301 Effective search space: 130032 Effective search space used: 130032 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: 50 (23.9 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