Alignments for a candidate for liuB in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Xanthobacter autotrophicus Py2

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_012113878.1 XAUT_RS09310 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= BRENDA::Q9I299
         (655 letters)



>NCBI__GCF_000017645.1:WP_012113878.1
          Length = 666

 Score =  691 bits (1783), Expect = 0.0
 Identities = 388/665 (58%), Positives = 462/665 (69%), Gaps = 20/665 (3%)

Query: 6   RSIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADS 65
           ++I+ LLVANRGEIA RVMR+A+A+GI +VAV+S  D +A HVA AD A  +G A   +S
Sbjct: 3   KAIRTLLVANRGEIAVRVMRTAKAMGIRTVAVYSQADANALHVASADEAYPIGPAPARES 62

Query: 66  YLRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAA 125
           YLR D I+ AA  SGA AIHPGYGFLSENA FA ACE+AG++F+GPPA+AI AMGSKSAA
Sbjct: 63  YLRIDAILDAARKSGADAIHPGYGFLSENAAFAEACEKAGIVFVGPPASAIRAMGSKSAA 122

Query: 126 KALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAE 185
           KALME+AGVPLVPGYHGE QD     REA RIG+PVL+KA+AGGGGKGMKVV   AE  +
Sbjct: 123 KALMEKAGVPLVPGYHGEDQDAGLLAREAERIGFPVLIKASAGGGGKGMKVVRSAAEFPD 182

Query: 186 ALSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVV 245
           AL+SAQREAK+AFGD R+LVEKYL  PRH+E+QVFAD HG+ +YL+ERDCSIQRRHQKVV
Sbjct: 183 ALASAQREAKSAFGDDRVLVEKYLTTPRHIEVQVFADSHGNAVYLHERDCSIQRRHQKVV 242

Query: 246 EEAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPV 305
           EEAPAPG+  E R AMG+AAV AA+A+GYVGAGTVEF+  E   F+FMEMNTRLQVEHPV
Sbjct: 243 EEAPAPGMTPERRAAMGKAAVDAAKAVGYVGAGTVEFIA-ESENFYFMEMNTRLQVEHPV 301

Query: 306 TEAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYR 365
           TE+ITG DLV WQI+VA+GE LPL Q  +PL+GHAIEVRLYAEDP  DFLP  GRL    
Sbjct: 302 TESITGQDLVEWQIKVAQGEKLPLAQADIPLHGHAIEVRLYAEDPARDFLPQVGRLDHLV 361

Query: 366 EAAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTN 425
                 G RVD+GVR GD VS  YDPM+AK+I  G  R EA +RL A LA T V GL TN
Sbjct: 362 LPFHLNGTRVDTGVRAGDTVSIHYDPMIAKIIVSGADRTEAVRRLDAALAATEVVGLATN 421

Query: 426 LAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQSEPGHRRD- 484
             FL+ I  HPAFAAAELDT FIARHQD LLP P+ + +     AA   L+ E     + 
Sbjct: 422 RVFLKAIATHPAFAAAELDTNFIARHQDLLLPPPEPVDDTVLALAALFVLKEEARQSAEA 481

Query: 485 ---DDPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRL---------DG 532
               DP SPW    GWR       DL    RD R  VR  H  PS + L         +G
Sbjct: 482 VDAADPWSPWGLAPGWRLNRDAHVDLTFADRDRRIAVR-AHFRPSGFILSLPGGDMSVEG 540

Query: 533 D-----DLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSA 587
           D      L +R+DGV   +  +R    L +   G    +E +DP   ++AA    G L A
Sbjct: 541 DAEADGTLRARLDGVALSARVIRTAAHLTVFVRGGEYGLEFIDPRLASQAATGTAGRLVA 600

Query: 588 PMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPL 647
           PM G+I+R+ VE GQ V  GA LVV+EAMKMEH++ AP  G VK L  + G+LV+EG  L
Sbjct: 601 PMPGTIIRIAVEEGQEVAEGAALVVVEAMKMEHTVAAPRDGKVKTLKFAVGDLVDEGAEL 660

Query: 648 VELDE 652
           + L++
Sbjct: 661 LVLED 665


Lambda     K      H
   0.319    0.135    0.397 

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: 1083
Number of extensions: 38
Number of successful extensions: 7
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: 655
Length of database: 666
Length adjustment: 38
Effective length of query: 617
Effective length of database: 628
Effective search space:   387476
Effective search space used:   387476
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 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 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