Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_086510703.1 BZY95_RS14935 amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_002151265.1:WP_086510703.1 Length = 401 Score = 144 bits (363), Expect = 4e-39 Identities = 108/334 (32%), Positives = 170/334 (50%), Gaps = 9/334 (2%) Query: 9 SRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNG 68 S L A+A A A +KI G TGP+ GA +A++QIN+ GG+ G Sbjct: 4 SVLAMAIAATSVAFVGAAQAEVKIGFIGGFTGPIESLTPPIYDGARLAVQQINEQGGILG 63 Query: 69 AQ-LEGVIYDDAC-DPKQAVAVANKVVN-DGVKFVVGHVCSSSTQPATDIYE-DEGVLMI 124 Q L D C D A A+++VN + V +VG +C+ +T A + GV+M+ Sbjct: 64 GQTLVMPSADTTCSDASAASNAADRMVNTENVTAIVGALCTGATVAAANSAAIPGGVVMV 123 Query: 125 TPSATAPEITSRGYK-LIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIAT 183 +P++TAP +T L+FRT+ D QG + K + ++ D+ +AV + YG G+A Sbjct: 124 SPASTAPAVTELDDNDLVFRTVPSDAYQGEILAKLMLDKGFDE-VAVTYVNNDYGRGLAD 182 Query: 184 EVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMG-LLLRQAKQ 242 E G VA G D+ + + L +G + + Y G +LRQA + Sbjct: 183 AFTAAFEAGGGMVAENLAHEDGRADYRSELGSLSASGAETLVVLAYADGSGQTILRQAYE 242 Query: 243 AGLDARFMGPEG-VGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSG 301 +G +F G +G VG+S I A+ D EGM+AT P + E P + +A +A + DP+ Sbjct: 243 SGAFTQFAGADGMVGSSLIEAVGADVLEGMIATRPGSPEL-PGTEIFAEAAEAADLDPTA 301 Query: 302 IFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRA 335 +F AY A ++A IE+ G A+ E +++ALR+ Sbjct: 302 VFAAQAYDAAFLLALAIEQNGSAEREGLSQALRS 335 Lambda K H 0.316 0.133 0.377 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: 341 Number of extensions: 17 Number of successful extensions: 7 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: 373 Length of database: 401 Length adjustment: 30 Effective length of query: 343 Effective length of database: 371 Effective search space: 127253 Effective search space used: 127253 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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