Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_011767451.1 AZO_RS18710 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000061505.1:WP_011767451.1 Length = 374 Score = 390 bits (1003), Expect = e-113 Identities = 189/371 (50%), Positives = 259/371 (69%), Gaps = 2/371 (0%) Query: 1 MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60 M+ + + A +A A+ + VVKIGH P++G AH+GKD E GAR+A+E+ NA+ Sbjct: 1 MKTPVACLLAATLALVGNSAALAQTVVKIGHAGPLTGPIAHFGKDGEMGARLAVEDANAR 60 Query: 61 GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120 G+T+GG+K+KFELV+EDD DP+ T AQ+L D V GVVGH+ SG +IPAS+VY G Sbjct: 61 GITLGGQKVKFELVSEDDQGDPRTATTVAQRLTDLGVKGVVGHVTSGASIPASRVYEQAG 120 Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180 +P VT ++T+P LT+ GYK TFR+IAND G A YA +TLK VAIIDDRTAYGQG Sbjct: 121 VPVVTPSSTSPKLTRQGYKVTFRVIANDLQQGEATAKYAAETLKAAKVAIIDDRTAYGQG 180 Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240 +AD F A +G++VV +FTTDK+TDF+AILT IKAK PDA+FYGGMD Q PMLRQ+ Sbjct: 181 LADAFADAAKQRGLQVVGREFTTDKSTDFLAILTKIKAKAPDAVFYGGMDAQAAPMLRQL 240 Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKY 300 QLG + Y GGDG+CT E+ KLA A + V C++ AKMPGGT + +++ +Y Sbjct: 241 RQLGSSAI-YLGGDGVCTGEMIKLAGDAMS-DKVYCSQASLPPAKMPGGTDFLSRFKQRY 298 Query: 301 PNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNP 360 +Y+PY+YDA +++AMK A+S +P Y P L + +FKGVT IAF+P G+++N Sbjct: 299 KADVLLYAPYSYDAATALIEAMKAADSSEPAKYLPALQRVAFKGVTGEIAFDPQGDIRNG 358 Query: 361 AITLYVYKDGK 371 ++++ ++DGK Sbjct: 359 GVSMHRFRDGK 369 Lambda K H 0.315 0.131 0.375 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: 438 Number of extensions: 10 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: 375 Length of database: 374 Length adjustment: 30 Effective length of query: 345 Effective length of database: 344 Effective search space: 118680 Effective search space used: 118680 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: 42 (22.0 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