Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= reanno::pseudo3_N2E3:AO353_21720 (220 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 103 bits (258), Expect = 4e-27 Identities = 66/207 (31%), Positives = 114/207 (55%), Gaps = 11/207 (5%) Query: 21 GFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVL-----VL 75 GF+ ++ V + L +GI L ++ +++ +RG P+ L V+ Sbjct: 224 GFMLNMMLGVTCVSLSVPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVM 283 Query: 76 ACFYMAPALGWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQA 135 ++ P +D F V+ +TLF +++AE++RG L ALP+GQ EA+ ++GL + QA Sbjct: 284 LSYFFPPDA--TVDLFLRVVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQA 341 Query: 136 LAYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELL-LSTQQIIART---FMTLEF 191 + ++LPQAL+ +P VN + + K +TL+SVI + +L+ + I+A T + E Sbjct: 342 MRLIILPQALKISIPGIVNVAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWEL 401 Query: 192 YLFAGFLFFIINYAIELLGRHIEKRVA 218 FA FLFFI+ Y I + +E+R+A Sbjct: 402 LGFAAFLFFIVCYGISQYSQWLERRLA 428 Lambda K H 0.330 0.142 0.440 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: 282 Number of extensions: 12 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: 432 Length adjustment: 27 Effective length of query: 193 Effective length of database: 405 Effective search space: 78165 Effective search space used: 78165 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 (21.9 bits) S2: 48 (23.1 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