Alignments for a candidate for pccB in Flavobacterium ummariense DS-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Flavobacterium ummariense DS-12

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_091518620.1 BM253_RS02600 acyl-CoA carboxylase subunit beta

Query= SwissProt::Q3J4E3
         (510 letters)



>NCBI__GCF_900115115.1:WP_091518620.1
          Length = 515

 Score =  667 bits (1720), Expect = 0.0
 Identities = 327/508 (64%), Positives = 400/508 (78%), Gaps = 7/508 (1%)

Query: 8   LENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCTDFGMQDD 67
           L  + A A+ GGG++R+ AQH + KLTARERIE   DEGSFEE   FV HR  DFG+  +
Sbjct: 10  LNKKLAEAKLGGGEKRITAQHAKKKLTARERIEYFFDEGSFEEIGAFVTHRTKDFGLDKE 69

Query: 68  RPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGAPVIGLND 127
              GDGV+TG+GT+NGR+VY F+QDFTVFGG+LSETHA+KICK+MDMA++ GAP+IGLND
Sbjct: 70  HYLGDGVITGYGTVNGRLVYAFAQDFTVFGGALSETHAEKICKVMDMALKVGAPMIGLND 129

Query: 128 SGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDFIFMVRDT 187
           SGGARIQEGV SL GYAD+F RN+ ASGVIPQIS IMGPCAGGAVYSPAMTDF  MV  +
Sbjct: 130 SGGARIQEGVRSLGGYADIFFRNVQASGVIPQISAIMGPCAGGAVYSPAMTDFTMMVEGS 189

Query: 188 SYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRRLVDFLPL 247
           SYMFVTGP+VVKTVTNE V+AEELGGASTH+ KS VA     ND+E L +++RL+ ++P 
Sbjct: 190 SYMFVTGPNVVKTVTNETVSAEELGGASTHSTKSGVAHTTSANDIECLEDVKRLLSYIPQ 249

Query: 248 SNRTPAPVRPF-FDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQKDFAAN 306
           +N+      PF F D   I D L+ ++PDN N+PYDM ++I  + DE  FYEI K++A N
Sbjct: 250 NNQEVVEDLPFEFGD--EIRDQLNNIVPDNANKPYDMHDVINNVIDEDSFYEIHKNYAEN 307

Query: 307 IITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVDVPGFLP 366
           II GF R+ G++VG+VAN PM LAGCLD++SS K+ARFVRFCDAFNIP+L LVDVPGFLP
Sbjct: 308 IIVGFARIGGKSVGIVANNPMFLAGCLDVNSSIKSARFVRFCDAFNIPLLVLVDVPGFLP 367

Query: 367 GTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNYAWPTAE 426
           GT QE+ G+I HGAKLL+A  EATVPKVTVITRKAYGGAYDVM SKH+  D N+AWP AE
Sbjct: 368 GTDQEWNGIIVHGAKLLYALSEATVPKVTVITRKAYGGAYDVMNSKHIGADMNFAWPGAE 427

Query: 427 IAVMGAKGATEILYRSELGD----KEKIAARAKEYEDRFANPFVAAERGFIDEVIMPHST 482
           IAVMGAKGA+EI+++ E+ +      K+A +  EY ++FANP+ AA+RGFIDEVI P  T
Sbjct: 428 IAVMGAKGASEIIFKREIAEAADPAAKLAEKETEYAEKFANPYRAAQRGFIDEVIFPQDT 487

Query: 483 RRRVSKAFASLRNKKLANPWKKHDNIPL 510
           RR++ KAF  L NK++A P +KH NIPL
Sbjct: 488 RRKLIKAFKMLENKEVATPNRKHGNIPL 515


Lambda     K      H
   0.321    0.138    0.404 

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: 827
Number of extensions: 24
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: 510
Length of database: 515
Length adjustment: 35
Effective length of query: 475
Effective length of database: 480
Effective search space:   228000
Effective search space used:   228000
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: 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 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