Alignments for a candidate for pccB in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Mycolicibacterium vanbaalenii PYR-1

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011781246.1 MVAN_RS20505 acetyl-CoA carboxylase subunit beta

Query= metacyc::MONOMER-17283
         (535 letters)



>NCBI__GCF_000015305.1:WP_011781246.1
          Length = 516

 Score =  695 bits (1794), Expect = 0.0
 Identities = 342/514 (66%), Positives = 401/514 (78%), Gaps = 8/514 (1%)

Query: 22  HQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSSFLEIGALAAYNV 81
           H +L   LR +LA    GG    R RH  RGKL  RDR+D L+DP S FLE+ ALAA  +
Sbjct: 11  HVALVDQLRTKLAAAALGGPERARERHVSRGKLLPRDRVDGLLDPGSPFLELAALAADGM 70

Query: 82  YDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQEIARENRLPCIY 141
           YD+E P AG++ GIGRV+GR  MI+ANDATVKGGTY+P+TVKKHLRAQEIA +N+LPCIY
Sbjct: 71  YDDECPGAGMIAGIGRVSGRECMIVANDATVKGGTYYPVTVKKHLRAQEIALQNQLPCIY 130

Query: 142 LVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCTAGGAYVPAMSDE 201
           LVDSGGA+LP Q EVFPDR+HFGRIFYNQA MSA+GI QIA V+GSCTAGGAYVPAMSDE
Sbjct: 131 LVDSGGAFLPRQDEVFPDREHFGRIFYNQATMSAKGIAQIAAVLGSCTAGGAYVPAMSDE 190

Query: 202 VVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFANDDREALAIVRD 261
            VIV+  GTIFLGGPPLVKAATGE VTAEELGG D+H+++SGV D+ A+DDR+AL IVR 
Sbjct: 191 AVIVRNQGTIFLGGPPLVKAATGEIVTAEELGGGDLHSKVSGVTDHLAHDDRDALRIVRR 250

Query: 262 IVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIARIVDGSRLHEFKT 321
           IV  L P+    WE+        D  E+Y ++P D R  YDV EVI RIVDG    EFK 
Sbjct: 251 IVGTLAPKADPPWEVAPTVDAVADQAELYDVVPVDSRVPYDVHEVITRIVDGGEFAEFKA 310

Query: 322 RYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELCCARNIPLVFLQNITGFMV 381
            YGTTLV GFA I G PVGI+ANNG+LF ESA+KGAHFIELC  R +PL+FLQNI+GFMV
Sbjct: 311 EYGTTLVTGFARIHGHPVGIVANNGVLFGESAVKGAHFIELCDKRVVPLLFLQNISGFMV 370

Query: 382 GKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMCGRAYQPRQLWMWPNAR 441
           G+ YE GGIAK GAK+VTAV+CA VPK TV+IGGS+GAGNY MCGRAY PR LWMWPNAR
Sbjct: 371 GRDYEAGGIAKHGAKMVTAVACARVPKLTVVIGGSYGAGNYSMCGRAYSPRFLWMWPNAR 430

Query: 442 ISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKYEQEGHPYYASARLWDD 501
           ISVMGG QAA+VL T+R         DMTP+E+E F API A+YE +G+PYY++ARLWDD
Sbjct: 431 ISVMGGEQAASVLATVR--------GDMTPDEEEAFKAPIRAQYEDQGNPYYSTARLWDD 482

Query: 502 GVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           GVIDP +TR V+ L L+  A+AP++P  +GVFRM
Sbjct: 483 GVIDPADTRTVVGLALSVTAQAPLEPVSYGVFRM 516


Lambda     K      H
   0.322    0.139    0.423 

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: 981
Number of extensions: 52
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: 535
Length of database: 516
Length adjustment: 35
Effective length of query: 500
Effective length of database: 481
Effective search space:   240500
Effective search space used:   240500
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 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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