Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 880 bits (2273), Expect = 0.0 Identities = 452/514 (87%), Positives = 470/514 (91%) Query: 1 MQAQTATRQHNIGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKI 60 M A T++ IGGSLRFNGIGK+FPGV+AL ISFVAHPGQVHALMGENGAGKSTLLKI Sbjct: 1 MHAHVQTQEQRIGGSLRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKI 60 Query: 61 LGGAYIPSSGDLQIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARF 120 LGGAY PSSGDLQIGEQ FK TADSI SGVAVIHQELHLVPEMTVAENLFLGHLPA F Sbjct: 61 LGGAYTPSSGDLQIGEQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASF 120 Query: 121 GLVNRGVLRQQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS 180 GL+NRGVLRQQAL LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS Sbjct: 121 GLINRGVLRQQALACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS 180 Query: 181 SLSAREIDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELT 240 SLSAREIDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGR+VRTFE+MS LT Sbjct: 181 SLSAREIDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALT 240 Query: 241 HDQLVTCMVGRDIQDIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVG 300 HDQLVTCMVGRDIQDIYDYR R RG VAL+V GLLGPGL EPVSF+ HKGEILGLFGLVG Sbjct: 241 HDQLVTCMVGRDIQDIYDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVG 300 Query: 301 AGRTELLRLLSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVG 360 AGRTEL R+LSGL R G L L +ELKL SPRDAIAAG+LLCPEDRKKEGI+PL SV Sbjct: 301 AGRTELFRMLSGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVA 360 Query: 361 ENINISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGR 420 ENINISAR +HST GCLLRG WE+ NADKQIK+LKVKTP A QKIMYLSGGNQQKAILGR Sbjct: 361 ENINISARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGR 420 Query: 421 WLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVL 480 WLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAA GIAVIVVSSDLMEVMGISDRILVL Sbjct: 421 WLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVL 480 Query: 481 CEGAMRGELSRDQANESNLLQLALPRQRVADAAN 514 CEGAMRGEL+R+QANESNLLQLALPRQRVAD AN Sbjct: 481 CEGAMRGELTREQANESNLLQLALPRQRVADVAN 514 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: 953 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: 514 Length adjustment: 35 Effective length of query: 479 Effective length of database: 479 Effective search space: 229441 Effective search space used: 229441 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 Apr 09 2024. 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