Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012589118.1 MSIL_RS00335 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000021745.1:WP_012589118.1 Length = 282 Score = 133 bits (335), Expect = 5e-36 Identities = 110/333 (33%), Positives = 160/333 (48%), Gaps = 65/333 (19%) Query: 18 LPLILQSFGNAWVRIADLALLYV--LLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMA 75 +P L F W + +A L V LLAL + +V+ G L LG AF +GAY AL++ Sbjct: 1 MPAALDDF--LWTYQSLIASLGVNGLLALSMYVVLAI-GQLSLGQAAFMGLGAYASALLS 57 Query: 76 SPHLADNFAAFAAMFPNGLHTSLW--IVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTL 133 LH+ L +V+ A L+ A F ++GAPTL+L G YLA+ T+ Sbjct: 58 ------------------LHSGLPFPLVLAAATLIPAAFALVIGAPTLRLSGVYLALATI 99 Query: 134 GFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLF 193 G GEI+RIFL D LT G GL I + F L G Sbjct: 100 GLGEILRIFLIQSD----LTGGALGLSGIPAKAGFALIYG-------------------C 136 Query: 194 LVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGA 253 L V +++++ R SR+GRA AIREDE AA G++ K+ A + A G++GA Sbjct: 137 LAAVTLALMLIAR---SRVGRAMEAIREDETAAAVSGVDLPRYKMAALVVSAMLAGLAGA 193 Query: 254 MFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQA 313 + F+ P + +V I++ +LGG+G G + GA++L+ LPE+LR PLQ Sbjct: 194 LNAHASSFIGPNDYGFDAAVTILSYALLGGVGSPFGPLAGALVLTLLPEILR----PLQD 249 Query: 314 MTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346 R ++ ++I +L P GL P Sbjct: 250 ----------FRLVVNGAIIVIAVLYMPHGLIP 272 Lambda K H 0.328 0.144 0.430 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: 247 Number of extensions: 15 Number of successful extensions: 2 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: 358 Length of database: 282 Length adjustment: 27 Effective length of query: 331 Effective length of database: 255 Effective search space: 84405 Effective search space used: 84405 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