Alignments for a candidate for liuB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Acidovorax sp. GW101-3H11

Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate Ac3H11_2275 Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3)

Query= SwissProt::Q99MR8
         (717 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2275
          Length = 682

 Score =  503 bits (1295), Expect = e-146
 Identities = 280/683 (40%), Positives = 401/683 (58%), Gaps = 20/683 (2%)

Query: 46  TKVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLA 105
           TK+LIANRGEIACRVI TA+KMG+ +VAVYS+AD+ + HV +ADEA  IG APS++SYL 
Sbjct: 3   TKILIANRGEIACRVIATARKMGIATVAVYSDADKEARHVKLADEAVHIGAAPSRESYLL 62

Query: 106 MEKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKSTSKSI 165
            +KII   K + AQA+HPGYGFLSEN  FA+ C+ EGI FIGP + +I  MG K  SK +
Sbjct: 63  ADKIIAACKQTGAQAVHPGYGFLSENEAFAKRCEDEGIAFIGPKAHSIAAMGDKIASKKL 122

Query: 166 MAAAGVPVVEGYHGKDQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQEQLE 225
              A V  + GY+      +   E A  IGYPVMIKA  GGGGKG+R+  +++E  E   
Sbjct: 123 ANEAKVNTIPGYNDAIAGPEQAVEIAKGIGYPVMIKASAGGGGKGLRVAFNDKEAFEGFA 182

Query: 226 SARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEA 285
           S + EA+ SF DD + IEKFV  PRH+E+QV GD HGN +YL ER+CS+QRRHQK+IEEA
Sbjct: 183 SCQNEARNSFGDDRIFIEKFVQEPRHIEIQVLGDSHGNVIYLNERECSIQRRHQKVIEEA 242

Query: 286 PAPGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHPVTEM 345
           P+P I+   R+ +GE AV+ AKAVKY  AGTVEF++    +FYF+EMNTRLQVEHPVTE 
Sbjct: 243 PSPFISDATRKAMGEQAVQLAKAVKYQSAGTVEFVVGKDQDFYFLEMNTRLQVEHPVTEC 302

Query: 346 ITGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHLSTPS 405
           ITG DLVE  +R+AAGEK+PL+Q ++   G A E RI AEDP  NF+P  G LV    P 
Sbjct: 303 ITGLDLVELMIRVAAGEKLPLTQADVKRDGWAIECRINAEDPFRNFLPSTGRLVRFQPPE 362

Query: 406 ADM---------STRIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKLRYCLHQYNI 456
             M           R++TGV +G E+ ++YD MIAKL+V  +DR  A++K+R  L+ + I
Sbjct: 363 ETMFQSDTTKKLGVRVDTGVYEGGEIPMYYDSMIAKLIVHGTDRNDAIAKMRAALNGFVI 422

Query: 457 VGLRSNVDFLLRLSGHPEFEAGNVHTDFIPQHHKDLLPSHSTIAKESVCQAALGLILKEK 516
            G+ SN+ F   L  HP+F  G+ +T FI +++     +      + +   AL   +  +
Sbjct: 423 RGISSNIPFQAALLAHPKFVTGDFNTGFIAENYGKGFHAEDVPHSDPMFLVALAAFMHRR 482

Query: 517 EMTSAFKLHTQDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIAVTYNRDGSYDMQIDN 576
               A  +    Q +      G    +  T     ++    + ++   ++ GS  +Q+ +
Sbjct: 483 YRARASGI--SGQLAGHEVKVGEEF-VVVTLGAEGQNQHHAVTVSDFEDKSGSSAIQVGD 539

Query: 577 KSFRV-----LGDLSSEDGCT---YLKSSINGVARKSKFILLDNTVHLFSMEGSIEVGIP 628
            S+++     LG +  +  C    +      GV +    + + +            +G  
Sbjct: 540 SSYQISSNATLGQIRVQGACNGQGFTAQVERGVGKNPLALRIAHNGTQIDTLVLSPLGAK 599

Query: 629 VPKYLSPVSAEGAQGGTIAPMTGTIEKVFVKAGDRVKAGDSLMVMIAMKMEHTIKAPKDG 688
           + K +   +        ++PM G +  V V+ G +V+AG+ L V+ AMKME+ + A +DG
Sbjct: 600 LHKLMPFKAPPDLSKFLLSPMPGLLVDVAVQPGQKVQAGEKLAVIEAMKMENILFAAQDG 659

Query: 689 RIKKVFFSEGAQANRHAPLVEFE 711
            + K+   +G        ++EF+
Sbjct: 660 VVGKITAGKGESLAVDQIILEFQ 682


Lambda     K      H
   0.318    0.133    0.382 

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: 1113
Number of extensions: 46
Number of successful extensions: 3
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: 717
Length of database: 682
Length adjustment: 39
Effective length of query: 678
Effective length of database: 643
Effective search space:   435954
Effective search space used:   435954
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources