GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens FW300-N1B4

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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 L-arabinose transport
           ATP-binding protein AraG (TC 3.A.1.2.2)
          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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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