Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_023430731.1 N177_RS02905 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000496075.1:WP_023430731.1 Length = 375 Score = 160 bits (406), Expect = 4e-44 Identities = 116/355 (32%), Positives = 176/355 (49%), Gaps = 11/355 (3%) Query: 3 KGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINK 62 +G + + AA+ G A A +T+KI GP++G +Q G R G +AI+Q N Sbjct: 9 RGARVAAIALAAVVATGAAD---AQETVKIGFIGPLSGGNSQQGLTARNGFQLAIDQANA 65 Query: 63 AGGVNGAQLEGVIYDDACDPKQAVAVANKVVND-GVKFVVGHVCSSSTQPATDIYEDEGV 121 + G ++EGVI DDA +P+ V+ A K+ ND V V GH S + G+ Sbjct: 66 REDL-GFKIEGVIQDDASNPQTGVSAALKLTNDPAVIAVTGHWNSPVALATAPVITRAGI 124 Query: 122 LMITPSATAPEITSRGYKLIFRTIG-LDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEG 180 + A +P+IT L+ R + L N P+A + AE + IA++ D YG Sbjct: 125 PFVIWGAISPKITETNNPLLARVVPTLVNTNEPLAA-WAAEEI-GQNIAIVSDTSDYGMA 182 Query: 181 IATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQA 240 +K E+AG + E G DF A ++K+K +YFGG E GL+ +Q Sbjct: 183 NVAAFRKPFEEAGGTITSVETAPVGTTDFRATLTKIKSDNPDAIYFGGVVTEAGLVRQQM 242 Query: 241 KQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKN-QDP 299 K+ GLD +G +G + E IAGDA+EG ++ + + E + K + +A+ A +P Sbjct: 243 KEVGLDVPMIGVDGFHDPEFIKIAGDAAEGTISGIMKETENE-KLVEMNEAYAAAGFAEP 301 Query: 300 SGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLK 354 G + AY A +I IE+AG D V EA+RA ++ G+ FDE G K Sbjct: 302 VGTYTKNAYDAANIIIAAIEEAG-TDRAAVGEAIRAMEYDGAMGHTSFDENGQTK 355 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: 321 Number of extensions: 14 Number of successful extensions: 5 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: 375 Length adjustment: 30 Effective length of query: 343 Effective length of database: 345 Effective search space: 118335 Effective search space used: 118335 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