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 beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_011778931.1 MVAN_RS08455 acyl-CoA carboxylase subunit beta

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_000015305.1:WP_011778931.1
          Length = 542

 Score =  745 bits (1923), Expect = 0.0
 Identities = 377/546 (69%), Positives = 436/546 (79%), Gaps = 4/546 (0%)

Query: 1   MSSATEPVGVPPAEAPDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERID 60
           M+S TEP         DIHTTAGKLADL +R  EA H   E AV K HAKGK TARERI 
Sbjct: 1   MTSVTEPSA---EHEIDIHTTAGKLADLRKRAAEAQHPVGETAVEKVHAKGKLTARERIL 57

Query: 61  MLLDEGSFVELDEHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSL 120
            LLDEGSFVELD  A+HRS NFG++ +RP GDGVVTG+GT+DGR VCVFSQD TVFGGSL
Sbjct: 58  ALLDEGSFVELDALAKHRSKNFGLEHNRPTGDGVVTGYGTIDGRDVCVFSQDATVFGGSL 117

Query: 121 GEVFGEKIVKVMDLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQI 180
           GEV+GEKIVKV +LA+KTG PL+GIND  GARIQEGV +LGLY+ IF  N  ASGVIPQI
Sbjct: 118 GEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFHNNIKASGVIPQI 177

Query: 181 SLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNER 240
           SLIMG  AGG VYSPA+TDF +MVDQTS MFITGPDVIKTVTGEDV+ E+LGGA TH  +
Sbjct: 178 SLIMGAAAGGHVYSPALTDFVIMVDQTSQMFITGPDVIKTVTGEDVTMEELGGAHTHMAK 237

Query: 241 SGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLELDAL 300
           SG  HY+A+ E DA+ YV++LLS+LP NN +  P +P    +   + + + D DLELD L
Sbjct: 238 SGTVHYVASGEQDALDYVRDLLSYLPPNNYAEPPRYPAPHAD-APIEESLTDEDLELDTL 296

Query: 301 VPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGT 360
           +PDSPNQPYDM EVITR++D+ EFLEV A +A N++ GFGR++G  VG+VANQP Q AG 
Sbjct: 297 IPDSPNQPYDMHEVITRILDDDEFLEVQAGYAGNIVIGFGRVDGRPVGIVANQPTQFAGC 356

Query: 361 LDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVP 420
           LDI+ASEKAARF+R CD FNIP++ LVDVPGFLPGT QE+NGIIRRGAKLLYAY EATV 
Sbjct: 357 LDINASEKAARFIRTCDCFNIPIVLLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVA 416

Query: 421 LVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGE 480
            VTVITRK+YGGAY VMGSK +GAD+ +AWPTAQIAVMGA GA   +YR+QL EAA  GE
Sbjct: 417 KVTVITRKSYGGAYCVMGSKDMGADVVVAWPTAQIAVMGASGAVGFVYRQQLREAAANGE 476

Query: 481 DVEALRARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKK 540
           DV+ALR +LQQEYEDTL NPY+AAERGYVD+VI PSHTRG+VA AL++L  K    P KK
Sbjct: 477 DVDALRLKLQQEYEDTLVNPYIAAERGYVDAVILPSHTRGYVATALKLLERKVVQTPPKK 536

Query: 541 HGNIPL 546
           HGNIPL
Sbjct: 537 HGNIPL 542


Lambda     K      H
   0.318    0.136    0.398 

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: 862
Number of extensions: 32
Number of successful extensions: 5
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: 546
Length of database: 542
Length adjustment: 35
Effective length of query: 511
Effective length of database: 507
Effective search space:   259077
Effective search space used:   259077
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: 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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