GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Pseudomonas simiae WCS417

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)



>lcl|FitnessBrowser__WCS417:GFF2162 PS417_11030 L-arabinose
           transporter ATP-binding protein
          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.

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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