Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF1302 PS417_06615 leucine ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__WCS417:GFF1302 Length = 375 Score = 186 bits (471), Expect = 1e-51 Identities = 128/371 (34%), Positives = 186/371 (50%), Gaps = 18/371 (4%) Query: 6 KLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIG 65 KL +A AG + A + +KIG P +G YG GA+ AI ++NA+G + Sbjct: 10 KLFAAMVLAGVAGHSFAAD-TIKIGIAGPKTGPVTQYGDMQFMGAKQAIADINAKG-GVD 67 Query: 66 GKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVT 125 GK + E DDA DPKQ A A K+ + V VVGHL S +T PAS +Y D G+ +T Sbjct: 68 GKML--EAKEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMIT 125 Query: 126 GAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVF 185 AAT+P +T GYK FR I D+A G Y D +K K VA++ D+ YG+G+A Sbjct: 126 PAATSPEITARGYKLIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIATAV 185 Query: 186 KKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGM 245 K+T KG KV + DF +I+ +K N D ++YGG P+ G +LRQ ++ G+ Sbjct: 186 KQTLEKKGTKVAVFEGLNAGDKDFSSIIQKLKQANVDFVYYGGYHPELGLILRQAKEKGL 245 Query: 246 GNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTA-----WKAKYDAKY 300 N K+ G +G+ I+++A GA G ++ S P A K K D Sbjct: 246 -NAKFMGPEGVGNDSISQIAQGASE-GLLVTLP--KSFDTDPANKAIVEEFAKNKQDPTG 301 Query: 301 PNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNP 360 P F YS A +I +K A S D + +FK T ++F+ G++K+ Sbjct: 302 PFVFPAYS-----AIEVIAGGIKAAKSEDTAKVAEAIHAGTFKTPTGDLSFDAKGDLKDF 356 Query: 361 AITLYVYKDGK 371 +Y + GK Sbjct: 357 KFVVYEWHFGK 367 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: 392 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: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 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 17 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