Align RhaQ (characterized, see rationale)
to candidate WP_084931761.1 HA51_RS02830 hypothetical protein
Query= uniprot:Q7BSH2 (337 letters) >NCBI__GCF_002095475.1:WP_084931761.1 Length = 323 Score = 167 bits (423), Expect = 3e-46 Identities = 98/289 (33%), Positives = 160/289 (55%), Gaps = 4/289 (1%) Query: 37 VLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAIIALASTA 96 ++I V S SP F NL + + A+IA M L++ISG IDLSV AL S Sbjct: 31 LIIVVTFSFLSPVFFTVPNLLNILQQSSINALIALGMTLVIISGGIDLSVGPTAAL-SAV 89 Query: 97 MGAAVQI-GIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFRGISYIVL 155 +GA + + G+ P +L +G G CGVF+G+LV+ L +VT+G +SLFR I+ I Sbjct: 90 LGATLMVAGVPVPVAILATLGIGALCGVFSGMLVAYAGLQPFIVTLGGLSLFRAIALIYT 149 Query: 156 GDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHATNFGRQVYAIGNNDFA 215 G P +F V + ++ V+A++ ++++ T G + A+G N+ A Sbjct: 150 GGNPVFGIPMEFRSIINSDVFGI-PTPIIIVAVIALVLWLVMNKTPLGEYILAVGGNEEA 208 Query: 216 ARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWELEVVTMVVLGGISI 275 AR +G+PV+R K +F+++G ++ +A++ L RLG+ P+I WEL+ + +GG S+ Sbjct: 209 ARVAGVPVKRTKVTVFIISGTLASLASLILIGRLGAAEPTIGNLWELDAIAAAAIGGASL 268 Query: 276 LGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVTIAI 324 +GG G +I A ++G + GL LLN+ + GL+II+ + I Sbjct: 269 MGGKGSIVGT-IIGAIILGALRNGLTLLNIQAFYQLLATGLIIIIAMLI 316 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: 281 Number of extensions: 14 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: 323 Length adjustment: 28 Effective length of query: 309 Effective length of database: 295 Effective search space: 91155 Effective search space used: 91155 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