Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate GFF201 PS417_01020 glutamine ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__WCS417:GFF201 Length = 219 Score = 135 bits (341), Expect = 5e-37 Identities = 81/212 (38%), Positives = 120/212 (56%), Gaps = 1/212 (0%) Query: 6 SWLHELWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLI 65 S L LWV+ L G ++ S L+I T+ G++ G++ T + A R Y++L Sbjct: 4 SGLELLWVSLPQLGKGAAQTLSISFLSIAFSTVGGVLYGVLRTLNNRLINAVLRVYLELF 63 Query: 66 RGTPVFVLVLACFYMAPAL-GWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEA 124 R PV V + F+ P G + +F VL L+L+ S V E+VRGAL +LPRGQ EA Sbjct: 64 RAIPVLVWLYLLFFGLPIFFGLSLPSFWCAVLVLSLWGASEVGEVVRGALHSLPRGQREA 123 Query: 125 SQAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIAR 184 +IGL+ Q GYVLLPQAL+++ P +N T I+K S+L +IGV +++ QQII R Sbjct: 124 GLSIGLSDPQLYGYVLLPQALKRMTPPTLNVYTRIIKTSSLAVLIGVVDVIKVGQQIIER 183 Query: 185 TFMTLEFYLFAGFLFFIINYAIELLGRHIEKR 216 T+ ++ Y FF I Y + + +E+R Sbjct: 184 TYESVLIYGVLFLFFFFICYPLSAASKVLERR 215 Lambda K H 0.330 0.142 0.443 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: 175 Number of extensions: 8 Number of successful extensions: 2 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: 220 Length of database: 219 Length adjustment: 22 Effective length of query: 198 Effective length of database: 197 Effective search space: 39006 Effective search space used: 39006 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 45 (21.9 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