Alignments for a candidate for liuB in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Brucella microti CCM 4915

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_015799645.1 BMI_RS05560 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::Q99MR8
         (717 letters)



>NCBI__GCF_000022745.1:WP_015799645.1
          Length = 667

 Score =  516 bits (1328), Expect = e-150
 Identities = 293/678 (43%), Positives = 409/678 (60%), Gaps = 23/678 (3%)

Query: 45  ITKVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYL 104
           I K+LIANRGEIACRVI++AKKMG+ +VAVYS+ADRN++HV MADEA  IGPAPS QSY+
Sbjct: 2   IKKILIANRGEIACRVIKSAKKMGIATVAVYSDADRNALHVKMADEAVHIGPAPSNQSYI 61

Query: 105 AMEKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKSTSKS 164
            ++KI+   K + A A+HPGYGFLSEN  FAE  K   + FIGPP +AI  MG K TSK 
Sbjct: 62  VIDKILAAIKETGADAVHPGYGFLSENPRFAEALKAANVTFIGPPVNAIDAMGDKITSKK 121

Query: 165 IMAAAGVPVVEGYHGK-DQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQEQ 223
           + A AGV  V G+ G  + +D+ +R  AG IGYPVMIKA  GGGGKGMRI  ++ E +E 
Sbjct: 122 LAAEAGVSTVPGHMGLIEDADEAVRI-AGSIGYPVMIKASAGGGGKGMRIAWNDEEAREG 180

Query: 224 LESARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIE 283
            + +R EAK SF DD + IEKFV  PRH+E+QV GD HGN VYL ER+CS+QRR+QK+IE
Sbjct: 181 FQLSRNEAKSSFGDDRIFIEKFVTQPRHIEIQVLGDQHGNVVYLGERECSIQRRNQKVIE 240

Query: 284 EAPAPGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHPVT 343
           EAP+P ++   R+ +GE AV  AKAV Y  AGTVEFI+D   NFYF+EMNTRLQVEHPVT
Sbjct: 241 EAPSPFLDEATRKAMGEQAVALAKAVGYYSAGTVEFIVDGNRNFYFLEMNTRLQVEHPVT 300

Query: 344 EMITGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHLST 403
           E+ITG DLVE  +R+A+GEK+  +Q ++ L G A E+R+YAEDP  NF+P  G L     
Sbjct: 301 ELITGIDLVEEMIRVASGEKLRFAQADVKLNGWAIESRLYAEDPYRNFLPSIGRLTRYRP 360

Query: 404 PSADMST-----RIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKLRYCLHQYNIVG 458
           P    +      R +TGV +G E+S++YDPMIAKL  W  DR SA+  + + L  + + G
Sbjct: 361 PVEGRNPDGTVIRNDTGVFEGGEISMYYDPMIAKLCTWGPDRISAIDAMGHALDAFEVEG 420

Query: 459 LRSNVDFLLRLSGHPEFEAGNVHTDFIPQHHKD----LLPSHSTIAKESVCQAALGLILK 514
           +  N+ FL  +  HP F  G + T FI + + D    +  S       +   A + L+ +
Sbjct: 421 IGHNLPFLSAVMDHPRFREGALTTAFIAEEYPDGFSGVKCSEDDARTLAAVAAEINLVAQ 480

Query: 515 EKEMTSAFKLHTQDQFSPFSFSSGRRLNIS-YTRNMTLRSGKSDIVIAVTYNRDGSYDMQ 573
            ++   + +L  Q      S ++   + +  Y+  + +  G+    I   +   GS  + 
Sbjct: 481 RRDTQISGRLSPQKH----SIANDWVVTLDGYSLPVRIAEGEGGTTI--NFIDGGSLPIA 534

Query: 574 IDNKSFRVLGDLSSEDGCTYLKSSINGVARKSKFILLDNTVHLFSMEGSIEVGIPVPKYL 633
            D      LG  +       +K S +G   + ++  +D   H+     + E+   +P  L
Sbjct: 535 SDWHPGSQLGSFTVGGKPIAVKVSRSGTGWRLRWRGMDVVAHVRKPRVA-ELAKLMPVKL 593

Query: 634 SPVSAEGAQGGTIAPMTGTIEKVFVKAGDRVKAGDSLMVMIAMKMEHTIKAPKDGRIKKV 693
            P +++      + PM G I  + VK G+ V+AG  L  + AMKME+ ++A +   +K++
Sbjct: 594 PPDTSKML----LCPMPGVITSILVKDGETVEAGQPLATVEAMKMENVLRAERRATVKRI 649

Query: 694 FFSEGAQANRHAPLVEFE 711
               G        ++EFE
Sbjct: 650 TAEAGCSLAVDELIMEFE 667


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: 1105
Number of extensions: 53
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 717
Length of database: 667
Length adjustment: 39
Effective length of query: 678
Effective length of database: 628
Effective search space:   425784
Effective search space used:   425784
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 2024 update 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