Align RhaQ (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 147 bits (372), Expect = 8e-40 Identities = 94/304 (30%), Positives = 158/304 (51%), Gaps = 11/304 (3%) Query: 31 LLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAII 90 LL +A ++ +F+SL S YF A A++A M ++I IDLSV +++ Sbjct: 592 LLAVLAGMVALFSSL-SEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVM 650 Query: 91 ALASTAMGAAV-QIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFRG 149 ALA+ AA+ Q G P + + TGL CG G + +LPS +V++G + RG Sbjct: 651 ALAAATSAAAILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRG 710 Query: 150 ISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHATNFGRQVYAI 209 +Y+V + +Y D + SF F+L +VL V+ ++L T FGR V I Sbjct: 711 SAYVVTDSRT--QYVGDAISWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGI 768 Query: 210 GNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWELEVVTMVV 269 G N+ A R +G+ ++ I+F +TG+++G+A + ++RL + P+ G EL+V+ VV Sbjct: 769 GTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVV 828 Query: 270 LGGISILGGFRHDRGVFVIAAF---VMGLVTFGLGLLNLPGIVMSIFIGLLIIVTIAIPI 326 +GG S++GG RG V AF ++ ++ GL + I G +I+ + + Sbjct: 829 IGGTSLMGG----RGSVVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDT 884 Query: 327 IARR 330 + +R Sbjct: 885 LRQR 888 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: 632 Number of extensions: 32 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: 892 Length adjustment: 35 Effective length of query: 302 Effective length of database: 857 Effective search space: 258814 Effective search space used: 258814 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: 52 (24.6 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