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 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.

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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 (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