Align RhaQ (characterized, see rationale)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 137 bits (345), Expect = 4e-37 Identities = 93/304 (30%), Positives = 164/304 (53%), Gaps = 11/304 (3%) Query: 32 LFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAIIA 91 + V VL+ + S+ + F NLS + ++A M ++++G IDLSV +I++ Sbjct: 31 MLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILS 90 Query: 92 LASTAMGAAVQIGIGTPGLVLIGIGTGLACG----VFNGVLVSVLKLPSIVVTIGTMSLF 147 +++ A+ + + P L ++ + L CG + NG LV+ +KLP +VT+GT++ Sbjct: 91 ISAVV---AMLVSL-MPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAV 146 Query: 148 RGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHATNFGRQVY 207 RG++ +V D FA+ G G V+ V + F V+AV + +L T G Q+Y Sbjct: 147 RGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSW-FVLRRTVLGLQIY 205 Query: 208 AIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRL-GSTRPSIAQGWELEVVT 266 A+G N AAR SGI V V ++ ++G+++G+ V ++RL + + Q +EL+ + Sbjct: 206 AVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIA 265 Query: 267 MVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVTIAIPI 326 V+LGG S +GG G ++ A ++ +++ GL LL + I I GL+II +A+ Sbjct: 266 AVILGGTSFVGGTGSIVGT-LVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDS 324 Query: 327 IARR 330 R+ Sbjct: 325 YRRK 328 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: 342 Number of extensions: 27 Number of successful extensions: 4 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: 333 Length adjustment: 28 Effective length of query: 309 Effective length of database: 305 Effective search space: 94245 Effective search space used: 94245 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