Align ABC transporter permease (characterized, see rationale)
to candidate WP_034632042.1 G496_RS0102100 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000429985.1:WP_034632042.1 Length = 303 Score = 182 bits (461), Expect = 1e-50 Identities = 109/311 (35%), Positives = 168/311 (54%), Gaps = 28/311 (9%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64 L QI+NGL G +YALIA+G+T+++G++ ++NFAHGE+ IGA CI + Sbjct: 6 LMQIVNGLSAGMIYALIAIGFTLIFGVLNVVNFAHGEMYTIGAFAGLVCINSLH------ 59 Query: 65 PGWVILLLATIIACVVAATLNFVIEKVAYRPLRS----------SPRLAPLITAIGMSIL 114 W L L I+A V+EKVA++P R + R A L++++ SIL Sbjct: 60 --WP-LALVIIVALAAGGVAGVVLEKVAFKPFRRFQDEASLKSRAMREATLLSSLAFSIL 116 Query: 115 LQTLAMIIWKPNYKPYPT-MLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNL 173 ++ + + + P L + P ++G + Q LILG + V L L Y++ HT + Sbjct: 117 IKEIIQHFFGAEMQTIPAGYLLNDPIKVGSLTFSTGQFLILGSSVVMLGGLQYVLFHTRI 176 Query: 174 GRAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGL 233 G A+RA + NP A +G+ D I ATF +G++L AGIM G MG+ P L Sbjct: 177 GLAIRAISNNPLGAKYVGLSVDKTIIATFAVGSMLGGAAGIMVGLYQGAIFPYMGYAPSL 236 Query: 234 KAFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIIL 293 KAF A V GG+ ++ GAVV ++LG+ E++ + + +T G ++D+ A+ LII L Sbjct: 237 KAFVAMVMGGLSSIPGAVVCALILGVCESMATNF---MTQG-----WSDMVAYSFLIITL 288 Query: 294 TLRPSGLLGER 304 P G+ G R Sbjct: 289 IFFPQGIFGAR 299 Lambda K H 0.327 0.142 0.419 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: 223 Number of extensions: 8 Number of successful extensions: 4 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: 309 Length of database: 303 Length adjustment: 27 Effective length of query: 282 Effective length of database: 276 Effective search space: 77832 Effective search space used: 77832 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: 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