Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_011188509.1 DP_RS06410 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000025945.1:WP_011188509.1 Length = 296 Score = 137 bits (344), Expect = 4e-37 Identities = 88/299 (29%), Positives = 163/299 (54%), Gaps = 22/299 (7%) Query: 2 EYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLG 61 + F+Q L+ G++ G++Y ++AIG+ ++Y G+INFA GE M+G +++ Sbjct: 4 QLFVQYLLAGITYGSMYAIVAIGFNIIYNTTGIINFAQGEFVMLGGMLSISL-------- 55 Query: 62 ITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQIL 121 + ++PL L + L +++ T G VE + R L++ L ++ +G+SI L+ + Sbjct: 56 LQFMPLPLAIGL--AVVLTMAVGGLVEILFIRWLKNPGVLRMIVITVGLSILLREIALHI 113 Query: 122 QGARSKPLQPILPGN----LTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTS-LGRA 176 G L P GN + ++ VS + + + + + ++ L +TS +GR Sbjct: 114 WGEGVYSL-PYFYGNEISTVVILGARVSPQILWVIGVCLLLVVLL---HLFFKTSPMGRE 169 Query: 177 QRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAG-MMVLLIYGVIDFYIGFLAGVKA 235 RAC +KK A L G+N +++ +F++ A + A+AG +M + Y D G +K Sbjct: 170 MRACAVNKKAALLCGINARNMVTFSFMLSAGIGALAGAVMSPITYTQYDS--GAALAIKG 227 Query: 236 FTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLG 294 FT A+LGG+G+L GA+ G+++G++EAF + ++D ++L+++L RP GL G Sbjct: 228 FTVAILGGLGNLFGAVAAGILLGVLEAFSVSVLPLAFQDAIAISLLLVILCVRPHGLFG 286 Lambda K H 0.329 0.144 0.425 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: 287 Number of extensions: 17 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: 301 Length of database: 296 Length adjustment: 27 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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