Align RhaQ (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 145 bits (367), Expect = 1e-39 Identities = 96/317 (30%), Positives = 172/317 (54%), Gaps = 9/317 (2%) Query: 21 LRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISG 80 L A +LF + +L+ VF + A+ FL A N + + +IA M +++ G Sbjct: 19 LLAFARKHRTILFLL-LLVAVFGA-ANERFLTARNALNILSEVSIYGIIAVGMTFVILIG 76 Query: 81 EIDLSVAAIIALASTAMGAAVQIGIG---TPGLVLIGIGT--GLACGVFNGVLVSVLKLP 135 ID++V +++A AS A V +G L+ + + T GLA G G V+ L +P Sbjct: 77 GIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVP 136 Query: 136 SIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAI 195 + +VT+G M+++RG + ++ + + ++G G ++++ V+F ++A + Sbjct: 137 AFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFL-PVPVVIFALVAAAGHV 195 Query: 196 LLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPS 255 L T +GRQVYA+G N AAR SG+ V+ + + ++ + G ++G++ L++RLGS Sbjct: 196 ALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAV 255 Query: 256 IAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIG 315 G+EL V+ VV+GG S+ GG G V+ A ++G+++ GL +L++ V + IG Sbjct: 256 AGTGYELRVIASVVIGGASLTGGSGGVGGT-VLGALLIGVLSNGLVMLHVTSYVQQVVIG 314 Query: 316 LLIIVTIAIPIIARRIK 332 L+I+ +A AR K Sbjct: 315 LIIVAAVAFDHYARTHK 331 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: 306 Number of extensions: 25 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: 332 Length adjustment: 28 Effective length of query: 309 Effective length of database: 304 Effective search space: 93936 Effective search space used: 93936 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