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 GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein

Query= uniprot:A0A165ZSX8
         (514 letters)



>lcl|FitnessBrowser__WCS417:GFF4164 PS417_21330 L-arabinose
           transporter ATP-binding protein
          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 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