Align RhaQ (characterized, see rationale)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 99.4 bits (246), Expect = 1e-25 Identities = 85/279 (30%), Positives = 142/279 (50%), Gaps = 28/279 (10%) Query: 68 MIAFAMALLVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGL----VLIGIGTGLACGV 123 ++A M ++++G IDLSV A++A ++ + VQ G P L +++ +GTG G+ Sbjct: 66 IVAVGMTFVILAGGIDLSVGAVVAFSTVLLAELVQRH-GWPPLAAIALVLAVGTGFGAGM 124 Query: 124 FNGVLVSVLKLPSIVVTIGTMSLFRGISYIVLGDQAYGKYP--ADFAYF----GQGYVVW 177 GVL+ +L VVT+ M L RG++ ++ D P A A G G ++ Sbjct: 125 --GVLIQRFRLQPFVVTLAGMFLARGVATLISVDSIDIDQPWLASVANLRLPLGGGSMLS 182 Query: 178 VFSFEFVLFIVLAVLFA--ILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTG 235 V + + LAV+ A +L A++FGR VYAIG ++ +AR G+PV+ ++ L+G Sbjct: 183 VGAL-----VALAVVAAGALLAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSG 237 Query: 236 IMSGIAAVCLTSRLGSTRPSIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGL 295 + +A V T + S A G EL+ + VV+GG + GG + G ++ V+GL Sbjct: 238 FCAALAGVVYTLYMLSGYSQHALGLELDAIAAVVIGGTVLAGGSGYVLGT-LLGVLVLGL 296 Query: 296 VTFGLGLLNLPGIVMS----IFIGLLIIVTIAIPIIARR 330 + L+ G + S I IG L++ + + RR Sbjct: 297 IQ---TLIVFDGELSSWWTRIVIGALLLAFCLLQRLFRR 332 Lambda K H 0.330 0.145 0.423 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: 302 Number of extensions: 25 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: 337 Length of database: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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