Align RhaQ (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 142 bits (358), Expect = 1e-38 Identities = 96/319 (30%), Positives = 167/319 (52%), Gaps = 17/319 (5%) Query: 18 GTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLV 77 G L+++A S E+ + +A++I SL SPYFL N+ + +++ M ++ Sbjct: 22 GRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVI 81 Query: 78 ISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSI 137 ++G IDLSV ++ L+ +G A++ P +L+G+ TG G+ +G+L+ +L + Sbjct: 82 LTGGIDLSVGSVAGLSGIVLGLALK-DYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAF 140 Query: 138 VVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEF---VLFIVLAVLFA 194 VVT+G M++ R ++YI G A +P+D + +V+ F VLF+ A L A Sbjct: 141 VVTLGMMAIGRSLAYIFSGQTAISGFPSDLSS-----IVYTDVFGIPTNVLFLGFAYLLA 195 Query: 195 I-LLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTR 253 L T GR +YAIG+N AAR +G+ V + ++++G ++ +A +++ S Sbjct: 196 WGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVD 255 Query: 254 PSIAQGWELEVVTMVVLGGISILGGFRHDRGVFV---IAAFVMGLVTFGLGLLNLPGIVM 310 P G EL+ + VV+GG S+ GG RG V I +M ++ GL LL + Sbjct: 256 PLTGNGMELDAIAAVVIGGASLYGG----RGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQ 311 Query: 311 SIFIGLLIIVTIAIPIIAR 329 IG +II+ + + + R Sbjct: 312 GSAIGSIIIMALLVERLVR 330 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: 343 Number of extensions: 26 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 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