Align RhaQ (characterized, see rationale)
to candidate SMc03001 SMc03001 ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__Smeli:SMc03001 Length = 334 Score = 454 bits (1169), Expect = e-132 Identities = 235/326 (72%), Positives = 273/326 (83%), Gaps = 1/326 (0%) Query: 7 QPEKRIIPDRLGTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEK 66 Q R IPDRL R+ SWE LLF VA++IF+ NSLASPYFLD WNLSDATFNFTEK Sbjct: 5 QISPRNIPDRLQGGGARLLKSWEALLFVVAIVIFLGNSLASPYFLDPWNLSDATFNFTEK 64 Query: 67 AMIAFAMALLVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNG 126 AMIAFAMAL++ISGEIDLSVA+IIALASTAMG AVQ+G TP LV IG+G GL CG+ NG Sbjct: 65 AMIAFAMALVIISGEIDLSVASIIALASTAMGYAVQLGFDTPALVAIGLGVGLLCGLVNG 124 Query: 127 VLVSVLKLPSIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLF 186 +L++ L LPSIVVTIGTMSLFRG+S+IVLGDQA+ YP FA+FGQGYV WVFSFEF LF Sbjct: 125 LLITGLGLPSIVVTIGTMSLFRGLSFIVLGDQAFTGYPESFAWFGQGYVWWVFSFEFTLF 184 Query: 187 IVLAVLFAILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLT 246 +VLAV++ +LLH TNFGR VYAIGNN+ AA FSG+ V RVK LFLLTG+M+G+A+VCLT Sbjct: 185 VVLAVIYGVLLHRTNFGRAVYAIGNNETAALFSGVRVGRVKFTLFLLTGLMAGLASVCLT 244 Query: 247 SRLGSTRPSIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLP 306 SRLGSTRPSIA GWELEVVTMVVLGG++ILGG GV V+AA +MG+VTFG GLLN+P Sbjct: 245 SRLGSTRPSIALGWELEVVTMVVLGGVNILGGSGTIPGV-VLAALIMGMVTFGFGLLNVP 303 Query: 307 GIVMSIFIGLLIIVTIAIPIIARRIK 332 GIVMSIFIGLL+I IA+PI+ +R + Sbjct: 304 GIVMSIFIGLLLISVIALPILWQRAR 329 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: 467 Number of extensions: 21 Number of successful extensions: 5 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: 334 Length adjustment: 28 Effective length of query: 309 Effective length of database: 306 Effective search space: 94554 Effective search space used: 94554 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