GapMind for catabolism of small carbon sources

 

Alignments 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)



>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.

Links

Downloads

Related tools

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 (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:

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. 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