Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__WCS417:GFF2162 Length = 500 Score = 825 bits (2130), Expect = 0.0 Identities = 424/492 (86%), Positives = 450/492 (91%) Query: 15 SLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQI 74 +LRF+GIGK+FPGV+AL ISF AHPGQVHALMGENGAGKSTLLKILGGAYIP+SG L I Sbjct: 5 ALRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLHI 64 Query: 75 GEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALT 134 GEQ MAFK ADSIASGVAVIHQELHLVPEM+VAENLFLGHLP+RFG+VNRG+LR+QAL Sbjct: 65 GEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRKQALA 124 Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 LKGLADEIDP EK+GRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII Sbjct: 125 CLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 184 Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFE+MS LTHDQLVTCMVGRDIQ Sbjct: 185 ARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGRDIQ 244 Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314 DIYDYRPRE G+VAL+V GLLGPGL EPVSF V KGEILGLFGLVGAGRTEL RLLSGLE Sbjct: 245 DIYDYRPREHGEVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLLSGLE 304 Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374 R G L L + L L+SPRDAIAAGVLLCPEDRKKEGIIPL SV ENINISAR +HST Sbjct: 305 RASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTF 364 Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 G LLR WE+GNAD+QI ++KVKTP A QKIMYLSGGNQQK+ILGRWLSMPMKVLLLDEP Sbjct: 365 GWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLDEP 424 Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494 TRGIDIGAKAEIYQIIHNLAA GIAVIVVSSDLMEVMGI+DRILVLCEGA+RGE +R+ A Sbjct: 425 TRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTREHA 484 Query: 495 NESNLLQLALPR 506 ESNLLQLALPR Sbjct: 485 TESNLLQLALPR 496 Lambda K H 0.320 0.138 0.391 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: 909 Number of extensions: 36 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: 514 Length of database: 500 Length adjustment: 34 Effective length of query: 480 Effective length of database: 466 Effective search space: 223680 Effective search space used: 223680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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