Alignments for a candidate for pccB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_322788369.1 HTA01S_RS20805 carboxyl transferase domain-containing protein

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_001592305.1:WP_322788369.1
          Length = 609

 Score =  208 bits (529), Expect = 5e-58
 Identities = 167/545 (30%), Positives = 252/545 (46%), Gaps = 45/545 (8%)

Query: 13  AEAPDIHTTA-GKLADLYRRNHEAVHA---GSERAVAKQHAKGKRTARERIDMLLDEGSF 68
           A AP  H    G   DL R      H        AVA++HA G RTARE I  L D+GSF
Sbjct: 83  AVAPAAHAQPPGPRDDLRRLQQRLAHTLDGARPEAVARRHALGLRTARENIADLCDDGSF 142

Query: 69  VELDEHA----RHRSTNFGMDADRPYGDGVVTGWGTVDG-------RRVCVFSQDFTVFG 117
           +E    A    R R +   + A+ P  DG+VTG G+V+G        R  V + D TV  
Sbjct: 143 LEYGALAVAAQRSRRSEEDLIANTP-ADGMVTGIGSVNGLIFGAEPSRTVVMAYDATVLA 201

Query: 118 GSLGEVFGEKIVKVMDLAMKTGCPLVGINDSGGARIQEGVAAL--GLYAEIFKRNTHASG 175
           G+ G     K  +++ +A+    P+V   + GG R  +    +  GL+   F      SG
Sbjct: 202 GTQGMRNHAKTDRLLGIALAQQLPVVLFAEGGGGRPGDTDMPIVAGLHVGSFAAFARLSG 261

Query: 176 VIPQISLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGAR 235
            +P + +  G C  G       +D  +   Q S++ + GP +++         ED+G + 
Sbjct: 262 QVPVVGIAAGRCFAGNAALLGCSDVIIATRQ-SNIGMGGPAMVEGGGLGVFRPEDIGPSA 320

Query: 236 THNERSGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADL 295
             +  +G    L  DE  A++  +  LSF                  +G + D +     
Sbjct: 321 VQHV-NGVIDLLVDDEPQAVATARHYLSFF-----------------QGRLPDWIAPNQQ 362

Query: 296 ELDALVPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPM 355
            L  +VP++  + YD R  +  LVD+G  L +   F   +     RIEG  VG++AN P+
Sbjct: 363 GLRDVVPENRLRVYDTRAAMDGLVDQGSLLMLRTCFGIGIHTALARIEGRPVGLMANNPL 422

Query: 356 QLAGTLDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYA 415
            L G +D DA++KAARF++ C+A  +P+++LVD PGF+ G   E    +R  ++L    A
Sbjct: 423 HLGGAIDADAADKAARFMQLCNAHGLPLVSLVDTPGFMVGPAMEERAQVRHVSRLFVTAA 482

Query: 416 EATVPLVTVITRKAYG-GAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAE 474
              VP  +V+ RK YG GA  +           +AWP+ +   MG +GA  + YR++L E
Sbjct: 483 SLRVPFFSVVLRKGYGLGAMGMTAGGFHAPVFTVAWPSGEFGAMGLEGAVRLGYRKEL-E 541

Query: 475 AAERGEDVEAL-RARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKR 533
           A   G   EAL  + LQ++  +             +D+VI P  TR  +AR    LA  R
Sbjct: 542 ALPEGPQREALFESLLQRQIANGSAQQMATTLE--IDAVIDPVQTREWLARG---LASAR 596

Query: 534 EALPA 538
            A PA
Sbjct: 597 VAEPA 601


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: 775
Number of extensions: 49
Number of successful extensions: 8
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: 609
Length adjustment: 36
Effective length of query: 510
Effective length of database: 573
Effective search space:   292230
Effective search space used:   292230
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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