Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__WCS417:GFF4164 Length = 499 Score = 815 bits (2106), Expect = 0.0 Identities = 421/497 (84%), Positives = 449/497 (90%) Query: 12 IGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGD 71 IG +LRFNGIGK FPGV+AL+ ISF A P +VHALMGENGAGKSTLLKILGGAY+PSSG Sbjct: 2 IGAALRFNGIGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGT 61 Query: 72 LQIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQ 131 LQIGEQTM FK ADSIA GVAVIHQELHLVPEMTVAENLFLGHLP RFG+VNR LR+Q Sbjct: 62 LQIGEQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFLGHLPTRFGVVNRSQLRKQ 121 Query: 132 ALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLM 191 AL LKGLADEIDP EK+GRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLM Sbjct: 122 ALACLKGLADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLM 181 Query: 192 AIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGR 251 AII RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTF++M+ L+HDQLVTCMVGR Sbjct: 182 AIITRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMNALSHDQLVTCMVGR 241 Query: 252 DIQDIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLS 311 DIQDIYDYR RE+G+VAL+V+GLLGPGL EPVS VHKGEILGLFGLVGAGRTEL RLLS Sbjct: 242 DIQDIYDYRQREQGEVALKVEGLLGPGLREPVSLNVHKGEILGLFGLVGAGRTELFRLLS 301 Query: 312 GLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSH 371 GL R GSL L + L+LRSPRDAIAAGVLLCPEDRKKEGIIPL SV ENINISAR +H Sbjct: 302 GLTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAH 361 Query: 372 STLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLL 431 ST G LLR WE NAD+QIK++KVKTP A QKIMYLSGGNQQKAILGRWLSMPMKVLLL Sbjct: 362 STFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLLL 421 Query: 432 DEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSR 491 DEPTRGIDIGAK+EIYQIIHNLAA GIAVIVVSSDLMEVMGISDRILV+ EGA+ GEL+R Sbjct: 422 DEPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTR 481 Query: 492 DQANESNLLQLALPRQR 508 DQA+E+ LLQLALPR R Sbjct: 482 DQADEARLLQLALPRSR 498 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: 876 Number of extensions: 37 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: 499 Length adjustment: 34 Effective length of query: 480 Effective length of database: 465 Effective search space: 223200 Effective search space used: 223200 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