Align RhaQ (characterized, see rationale)
to candidate Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409 Length = 322 Score = 155 bits (391), Expect = 2e-42 Identities = 99/329 (30%), Positives = 165/329 (50%), Gaps = 12/329 (3%) Query: 6 TQPEKRIIPDRLGTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTE 65 T K + R LRR W +LL AV IFV +L FL N+ + Sbjct: 2 TVQNKALPTPRKPLDLRRFLDDWVMLLAAVG--IFVLCTLLIDNFLSPLNMRGLGLAIST 59 Query: 66 KAMIAFAMALLVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGT----GLAC 121 + A M + SG DLSV ++IA A G + + V +G+ GL Sbjct: 60 TGIAACTMLYCLASGHFDLSVGSVIACA----GVVAAVVMRDTDSVFLGVSAALVMGLIV 115 Query: 122 GVFNGVLVSVLKLPSIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSF 181 G+ NG++++ L++ +++ T+ TM + RG++YI +A G F FG G + V Sbjct: 116 GLINGIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQEQFFVFGNGQLFGV-PV 174 Query: 182 EFVLFIVLAVLFAILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIA 241 ++ IV + F LL+ T +GR AIG N AA +G+ V+R K+++F + G++ +A Sbjct: 175 PILITIVCFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKTLIFAVHGVIGALA 234 Query: 242 AVCLTSRLGSTRPSIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLG 301 V L SR+ S +P I QG+EL V++ VLGG+S+ GG R V + ++ ++ + Sbjct: 235 GVILASRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHV-IAGVLILAIIENAMN 293 Query: 302 LLNLPGIVMSIFIGLLIIVTIAIPIIARR 330 L N+ + G ++++ + I + +R Sbjct: 294 LKNIDTFYQYVIRGSILLLAVVIDRLKQR 322 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: 283 Number of extensions: 13 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: 322 Length adjustment: 28 Effective length of query: 309 Effective length of database: 294 Effective search space: 90846 Effective search space used: 90846 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