Align RhaQ (characterized, see rationale)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 169 bits (429), Expect = 7e-47 Identities = 104/304 (34%), Positives = 166/304 (54%), Gaps = 5/304 (1%) Query: 21 LRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISG 80 L+R + + V ++ VF AS FL N+ + + A+IA M ++++G Sbjct: 31 LKRSTLFYPFIGLLVVCIVMVF---ASDSFLSGANIENVLRQVSINAIIAVGMTCVILTG 87 Query: 81 EIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVT 140 IDLSV +++ALA T + G+ + IGI GL G NG V+ +P I+VT Sbjct: 88 GIDLSVGSVMALAGTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVT 147 Query: 141 IGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHAT 200 + TM + RG++ I G P ++FG G ++ V + V+ V+ V+ +LL Sbjct: 148 LATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKILGVQA-PVVIMAVIYVIAWVLLERM 206 Query: 201 NFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGW 260 FGR VYAIG N+ A R SG+ V RVK I++ + G+ S AA+ LT+RL S +P+ G+ Sbjct: 207 PFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGVGF 266 Query: 261 ELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIV 320 EL+ + VV+GG SI GG G +I A ++G++ GL ++ + V ++ G +I++ Sbjct: 267 ELDAIAAVVMGGTSISGGRGSIIGT-LIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILL 325 Query: 321 TIAI 324 I I Sbjct: 326 AIYI 329 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: 331 Number of extensions: 23 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: 335 Length adjustment: 28 Effective length of query: 309 Effective length of database: 307 Effective search space: 94863 Effective search space used: 94863 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 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