Align RhaQ (characterized, see rationale)
to candidate 1936623 b4460 fused L-arabinose transporter subunits of ABC superfamily: membrane components (RefSeq)
Query= uniprot:Q7BSH2 (337 letters) >FitnessBrowser__Keio:1936623 Length = 328 Score = 164 bits (416), Expect = 2e-45 Identities = 94/293 (32%), Positives = 161/293 (54%), Gaps = 6/293 (2%) Query: 32 LFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAIIA 91 + V ++F+ ++ P F N+ + M+A M + SG+ DLSVA++IA Sbjct: 27 MLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIA 86 Query: 92 LASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFRGIS 151 A + + V G+ G+ CG+ NG +++ LK+ +++ T+ TM + RG++ Sbjct: 87 CAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVRGLA 146 Query: 152 YIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLA--VLFAILLHATNFGRQVYAI 209 YI+ +A G D ++F GY W F +++ +A ++F +LL+ T FGR AI Sbjct: 147 YIISDGKAVGI--EDESFFALGYANW-FGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAI 203 Query: 210 GNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWELEVVTMVV 269 G N+ AAR +G+PV R K I+F+L+G++S IA + L SR+ S +P + G+EL V++ V Sbjct: 204 GGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISACV 263 Query: 270 LGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVTI 322 LGG+S+ GG V V ++G V + LLN+ + GL+++ + Sbjct: 264 LGGVSLKGGIGKISYV-VAGILILGTVENAMNLLNISPFAQYVVRGLILLAAV 315 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: 332 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: 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