Align leucine-specific-binding protein LivK (characterized)
to candidate WP_084936137.1 HA51_RS18910 branched-chain amino acid ABC transporter substrate-binding protein
Query= CharProtDB::CH_107418 (369 letters) >NCBI__GCF_002095475.1:WP_084936137.1 Length = 375 Score = 553 bits (1424), Expect = e-162 Identities = 266/369 (72%), Positives = 314/369 (85%), Gaps = 5/369 (1%) Query: 6 KTIIAGMIALAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIKGD 65 + ++AG +ALA+SH A+A DIK+A+VGA +GP+AQ+GDM+F GA QAIKDINAKGG+ GD Sbjct: 7 RALLAGCVALALSHAALAKDIKIAIVGAATGPVAQYGDMQFTGAAQAIKDINAKGGVNGD 66 Query: 66 KLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPGAT 125 KLVGVEYDDACDPKQAVAVANK+VNDGIKYVIGHLCSSSTQPASDIY DEGILMI+P AT Sbjct: 67 KLVGVEYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYNDEGILMITPAAT 126 Query: 126 NPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGL 185 PELT RGY ++RT GLDS QGPTAA YIL +KP+RIA++HDKQQYG+GLA SVQ L Sbjct: 127 APELTARGYADVLRTTGLDSDQGPTAATYILNEIKPKRIAVVHDKQQYGQGLAESVQKTL 186 Query: 186 KAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTQF 245 KA NVV F+GITAG+KDFS LIARLKKEN+DFVYYGGYYPE+GQ+LRQA++ GL F Sbjct: 187 KAKGGNVVLFEGITAGDKDFSTLIARLKKENVDFVYYGGYYPELGQILRQAKAAGLNAGF 246 Query: 246 MGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANQGIVDALKA----DKKDPSGPYVW 301 MGPEGVGNASLSNIAGDA+EG+ VT+PKRYDQ P N+ IV+A+KA ++KDP+GP+VW Sbjct: 247 MGPEGVGNASLSNIAGDASEGLYVTLPKRYDQLPENKAIVEAIKANTASNRKDPTGPFVW 306 Query: 302 ITYAAVQSLATALERTGSDEPLALVKDLKANGA-NTVIGPLNWDEKGDLKGFDFGVFQWH 360 TYAA+QSL +ER+ S EP A+ K+LK A TV+G LNWD+KGDLKGF+FGVF+WH Sbjct: 307 TTYAAIQSLVAGIERSKSAEPDAIAKNLKEGAAVPTVMGNLNWDQKGDLKGFEFGVFKWH 366 Query: 361 ADGSSTAAK 369 DGSSTA K Sbjct: 367 KDGSSTAVK 375 Lambda K H 0.315 0.133 0.386 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: 570 Number of extensions: 15 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: 369 Length of database: 375 Length adjustment: 30 Effective length of query: 339 Effective length of database: 345 Effective search space: 116955 Effective search space used: 116955 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 (21.5 bits) S2: 49 (23.5 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