Align RhaQ (characterized, see rationale)
to candidate WP_108223269.1 C8J29_RS11820 ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >NCBI__GCF_003046325.1:WP_108223269.1 Length = 363 Score = 141 bits (356), Expect = 2e-38 Identities = 93/310 (30%), Positives = 155/310 (50%), Gaps = 16/310 (5%) Query: 30 VLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAI 89 V L + V + +F +L F A+ L+ ++ A L+V++ IDLSV AI Sbjct: 46 VPLIVLVVSVSIFGALLGQKFFSAFTLTLILQQVAIVGIVGAAQTLVVLTAGIDLSVGAI 105 Query: 90 IALASTAMGA-AVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFR 148 + L+S MG + GI P VL G+ G G NG LV+ +KLP +VT+G + Sbjct: 106 MVLSSVIMGQFTFRYGIPAPLSVLCGLAAGAGIGFVNGTLVARMKLPPFIVTLGMWQIVL 165 Query: 149 GISYI-----VLGDQAYGKYPADFAYFGQGYVVW---------VFSFEFVLFIVLAVLFA 194 +++ + Q +FG + + VF++ VL I+L ++ A Sbjct: 166 AANFLYSANETIRSQDISAQAPILQFFGNTFRLGADEAGRGGAVFTYGAVLLILLVLVIA 225 Query: 195 ILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRP 254 +L T +GR VYA+G++ AA +G+ V ++ L+G++ +A + RLGS P Sbjct: 226 YVLRQTAWGRHVYAVGDDPDAAELAGVQTRNVLVTVYTLSGLICALAGWVMIGRLGSVSP 285 Query: 255 SIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFI 314 + Q +E +T VV+GGIS+ GG G+ + A ++G+ + GL L+ + I Sbjct: 286 TAGQFANIESITAVVIGGISLFGGRGSVLGM-LFGALIVGVFSLGLKLMGTDPQWTYLLI 344 Query: 315 GLLIIVTIAI 324 G+LII +A+ Sbjct: 345 GMLIIAAVAV 354 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: 321 Number of extensions: 14 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: 337 Length of database: 363 Length adjustment: 29 Effective length of query: 308 Effective length of database: 334 Effective search space: 102872 Effective search space used: 102872 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 24 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