Alignments for a candidate for liuB in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Cereibacter sphaeroides ATCC 17029

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_011840651.1 RSPH17029_RS04405 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::Q99MR8
         (717 letters)



>NCBI__GCF_000015985.1:WP_011840651.1
          Length = 666

 Score =  533 bits (1372), Expect = e-155
 Identities = 297/686 (43%), Positives = 407/686 (59%), Gaps = 44/686 (6%)

Query: 47  KVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLAM 106
           K+LIANRGEIACRVI+TA+KMG+Q+VAVYS+ADRN++HV MADEA  IGP P+ QSY+ +
Sbjct: 4   KILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYIVI 63

Query: 107 EKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKSTSKSIM 166
           +KI++  K+S A+A+HPGYGFLSE M+FA   +  G++FIGPPS AI  MG K TSK + 
Sbjct: 64  DKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKKLA 123

Query: 167 AAAGVPVVEGYHGKDQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQEQLES 226
             AGV  V GY G         + + +IGYPVMIKA  GGGGKGMRI  SE E +E  ES
Sbjct: 124 KEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGFES 183

Query: 227 ARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAP 286
           ++ EA  SF DD + IEKFV  PRH+E+QV  D+HGN VYL ER+CS+QRR+QK+IEEAP
Sbjct: 184 SKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADNHGNCVYLHERECSIQRRNQKVIEEAP 243

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

Query: 347 TGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHLSTPSA 406
           TG DLVE  +R+AAGEK+P  Q ++ + G A E+R+YAEDP  NF+P  G L     P  
Sbjct: 304 TGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRPPVE 363

Query: 407 DMS----TRIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKLRYCLHQYNIVGLRSN 462
            ++     R +TGV +G E+S++YDPMIAKL  WA  R++A+ ++R  L  + + G+  N
Sbjct: 364 SVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGIGHN 423

Query: 463 VDFLLRLSGHPEFEAGNVHTDFIPQHHKD----LLPSHSTIAKESVCQAALGLILKEKEM 518
           + F+  +  HP F  G++ T FI + + D     +    T+ + +   AA+  +      
Sbjct: 424 LPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRV------ 477

Query: 519 TSAFKLHTQDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIA---------VTYNRDGS 569
                            +  RR  IS T N   R    D V+A         +  +R+GS
Sbjct: 478 -----------------AEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGS 520

Query: 570 YDMQIDNKSFRVLGDLSSEDGCTYLKSSINGVARKSKFILLDNTVHLFSMEGSIEVGIPV 629
                D  S RV  D +       L      +  K   I +   + L   +  + V  P 
Sbjct: 521 TVSFSDGSSLRVTSDWTPGQPLASLMVDGKPLVMKVGKIPMGFRLRLRGADLKVNVRTPR 580

Query: 630 PKYLSPVSAEGAQGGT----IAPMTGTIEKVFVKAGDRVKAGDSLMVMIAMKMEHTIKAP 685
              L+ +  E     T    + PM G + K+ V  GD V+ G +L  + AMKME+ ++A 
Sbjct: 581 QAELALLMPEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAE 640

Query: 686 KDGRIKKVFFSEGAQANRHAPLVEFE 711
           + G +KK+  + GA       ++EFE
Sbjct: 641 RRGTVKKIAAAPGASLRVDDVIMEFE 666


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: 1087
Number of extensions: 39
Number of successful extensions: 4
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: 666
Length adjustment: 39
Effective length of query: 678
Effective length of database: 627
Effective search space:   425106
Effective search space used:   425106
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 Apr 10 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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