Alignments for a candidate for liuB in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Sedimenticola selenatireducens DSM 17993

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 WP_029132303.1 A3GO_RS0103980 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::Q99MR8
         (717 letters)



>NCBI__GCF_000428045.1:WP_029132303.1
          Length = 660

 Score =  525 bits (1351), Expect = e-153
 Identities = 293/675 (43%), Positives = 421/675 (62%), Gaps = 28/675 (4%)

Query: 47  KVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLAM 106
           K+LIANRGEIACRVI++A+KMG+++VAV+S+ADR ++HV MADEA  IGP+ S +SYL M
Sbjct: 4   KILIANRGEIACRVIKSARKMGIKTVAVFSDADREALHVKMADEAVHIGPSASAESYLVM 63

Query: 107 EKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKSTSKSIM 166
           E+IIQ  + + AQA+HPGYGFLSEN  F E  ++EGI FIGP + AI  MG K TSK++ 
Sbjct: 64  ERIIQACRDTGAQAVHPGYGFLSENSAFCEALEKEGIAFIGPATLAINSMGDKITSKNLA 123

Query: 167 AAAGVPVVEGYHGKDQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQEQLES 226
             AGV V+ GY    +  +   E +  IGYPVM+KA  GGGGKGMR+  +E E ++  E 
Sbjct: 124 EQAGVNVIPGYTDVVRDAEHAVEISNGIGYPVMLKASAGGGGKGMRVAWNEAECRDGFER 183

Query: 227 ARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAP 286
           A  EA+ SF DD + IEKF++ PRH+E+QV  D HGN +YL ER+CS+QRRHQK+IEEAP
Sbjct: 184 ATNEARSSFGDDRVFIEKFIEEPRHIEIQVMADTHGNVIYLGERECSIQRRHQKVIEEAP 243

Query: 287 APGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHPVTEMI 346
           +P I+   R+++GE AV+ A+AV+Y  AGTVEFI+D++ NFYF+EMNTRLQVEHPVTE++
Sbjct: 244 SPFIDEATRKQMGEQAVQLARAVQYRSAGTVEFIVDAKRNFYFLEMNTRLQVEHPVTELV 303

Query: 347 TGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHLSTPSA 406
           TG DLVE  +R+A GE++PL QE++ L G A E+R+YAEDP  NF+P  G LV    P  
Sbjct: 304 TGQDLVELMIRVANGEELPLRQEDVKLTGWAMESRVYAEDPFRNFLPSIGRLVKYEPPVG 363

Query: 407 DMSTRIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKLRYCLHQYNIVGLRSNVDFL 466
           D + R++TGV +G EVS+ YDPMIAKL+ + ++R  A+++++  L  Y I G++ N+ FL
Sbjct: 364 D-NVRVDTGVYEGGEVSMFYDPMIAKLITYGANRNEAITRMQDALDAYCIRGVQHNISFL 422

Query: 467 LRLSGHPEFEAGNVHTDFIPQHHKDLLPSHSTIAKESVCQAALGLILKEKEMTSAFKLHT 526
             L  HP F  G + T+FI +   D   +      +     A+  ++  + M  A +L  
Sbjct: 423 NALMVHPRFIEGRLTTNFIAEEFPDGFDASYVPQDDPAKVVAVAAMIHRQYMDRAARLSG 482

Query: 527 QDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIAVTYNRDGSYDMQIDNKSFRVLGDLS 586
           Q +         R++N  +   + + +G+   V AV  N  G   ++     + V  + +
Sbjct: 483 QLR------GHERKVNDEW---VVIINGEHHAVSAVPAN--GGCRVEYAGNGYDVTTEWA 531

Query: 587 SEDGCTYLKSSING------VARKSKFILL----DNTVHLFSMEGSIEVGIPVPKYLSPV 636
              G   L  +ING      V RK  ++ L    + T  L     + E+   +P+  +P 
Sbjct: 532 L--GQPLLHGTINGLSVCFQVERKGLWLRLFHRGNQTDALVMTPRAAELHALMPEKEAPD 589

Query: 637 SAEGAQGGTIAPMTGTIEKVFVKAGDRVKAGDSLMVMIAMKMEHTIKAPKDGRIKKVFFS 696
            ++      ++PM G + KV V  G  VKAG+ L V+ AMKME+ ++A +D  +  +   
Sbjct: 590 LSK----FLLSPMPGLLVKVSVVEGQEVKAGEELAVIEAMKMENVLRAEQDATVASIQAE 645

Query: 697 EGAQANRHAPLVEFE 711
            G        ++EFE
Sbjct: 646 AGDSLRVDQVIIEFE 660


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: 1099
Number of extensions: 47
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: 660
Length adjustment: 39
Effective length of query: 678
Effective length of database: 621
Effective search space:   421038
Effective search space used:   421038
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 24 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:

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