Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_068168777.1 HTA01S_RS07615 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_001592305.1:WP_068168777.1 Length = 395 Score = 425 bits (1093), Expect = e-124 Identities = 223/392 (56%), Positives = 272/392 (69%), Gaps = 18/392 (4%) Query: 1 MQLKLKLTVVAA----------------IAAAAGVASAQEQVVKIGHVAPVSGAQAHYGK 44 MQL +KL V+AA + A A +A QV+KIGHV P SGA AH GK Sbjct: 1 MQLNIKLAVIAAAVALAACGKKEEAAAPVEAPAAAPAADAQVIKIGHVGPTSGAIAHLGK 60 Query: 45 DNENGARMAIEELNAQGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHL 104 DNENGA+MAIEELNA G+TIGG KFEL+AEDDAADPKQGTAAA KL DAKVAGV+GHL Sbjct: 61 DNENGAKMAIEELNAAGLTIGGAPAKFELLAEDDAADPKQGTAAATKLVDAKVAGVIGHL 120 Query: 105 NSGTTIPASKVYNDCGIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLK 164 NSGTTIPAS++YND GIP ++ +ATNP T+ GY FR++A+D LG L YAV+TLK Sbjct: 121 NSGTTIPASQIYNDAGIPQISPSATNPKYTRQGYAGVFRMVADDVHLGGTLGKYAVETLK 180 Query: 165 LKTVAIIDDRTAYGQGVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAI 224 KTVA+IDDRTAYGQGVAD F+K A G VV +FT DKATDF AILT +KAK PD + Sbjct: 181 AKTVAVIDDRTAYGQGVADEFEKGVAAAGGTVVGREFTNDKATDFNAILTTLKAKKPDVV 240 Query: 225 FYGGMDPQGGPMLRQMEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAE-GGSSL 283 F+GGMD GPML+QM+QLG+ N K+ GGDGIC+SE+ KLAA V CAE GG Sbjct: 241 FFGGMDAVAGPMLKQMKQLGI-NAKFMGGDGICSSELPKLAADGMADEQVYCAEAGGVEG 299 Query: 284 AKMPGGTAWKAKYDAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFK 343 + G ++A + AK+ QVY+PY YDA ++ +AM A S DP Y P L +++K Sbjct: 300 EQKEGMDKFRADFKAKFGADVQVYAPYVYDAVKVMANAMVTAGSADPAKYLPALKATNYK 359 Query: 344 GVTSTIAFEPNGEMKNPAITLYVYKDGKKTPL 375 GVT IAF+ G++KN A+TL YK G +T + Sbjct: 360 GVTGNIAFDEKGDIKNGALTLMTYKGGARTTI 391 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: 560 Number of extensions: 17 Number of successful extensions: 4 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: 395 Length adjustment: 30 Effective length of query: 345 Effective length of database: 365 Effective search space: 125925 Effective search space used: 125925 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