Align RhaQ (characterized, see rationale)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 171 bits (434), Expect = 2e-47 Identities = 105/298 (35%), Positives = 166/298 (55%), Gaps = 9/298 (3%) Query: 31 LLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAII 90 L A V++ + LAS F N + + ++A M+ ++++G IDLSV A + Sbjct: 31 LPLAGLVVVSLLMGLASDNFFTLSNWFNVLRQVSIVGILAVGMSFVILTGGIDLSVGAAM 90 Query: 91 ALAST-AMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFRG 149 ALA T + G V G+ P +L G+G G+ NG LV+ ++P+I+VT+ TM + RG Sbjct: 91 ALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARG 150 Query: 150 ISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHATNFGRQVYAI 209 + I G P ++FG G + V +L +++ L +LL T FGR VYAI Sbjct: 151 VGLIYSGGYPISGLPGWISWFGVGRIGMV-PVPVILMLIVYALAWLLLQRTAFGRHVYAI 209 Query: 210 GNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWELEVVTMVV 269 G N+ AAR SG+ R+K ++ ++G SG+AA+ LT RL S +P+ G+EL+ + VV Sbjct: 210 GGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVV 269 Query: 270 LGGISILGGFRHDRGVFV---IAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVTIAI 324 LGG +I GG RG+ V I A ++G++ GL L+ + + I G++I++ I I Sbjct: 270 LGGTAIAGG----RGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYI 323 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: 367 Number of extensions: 21 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: 328 Length adjustment: 28 Effective length of query: 309 Effective length of database: 300 Effective search space: 92700 Effective search space used: 92700 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