Alignments for a candidate for pccB in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Bacteroides thetaiotaomicron VPI-5482

Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate 351445 BT1917 propionyl-CoA carboxylase beta chain (NCBI ptt file)

Query= SwissProt::I3R7F1
         (516 letters)



>FitnessBrowser__Btheta:351445
          Length = 511

 Score =  609 bits (1570), Expect = e-179
 Identities = 300/506 (59%), Positives = 384/506 (75%), Gaps = 6/506 (1%)

Query: 11  REKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHKFGMEETK 70
           +E+   A  GGG ++I  QH+ GKMTARERI+  LD GTF E D+   HR   +GM++ K
Sbjct: 12  QERDRIASLGGGVEKIEKQHESGKMTARERIEMLLDKGTFVELDKLMVHRCTNYGMDKNK 71

Query: 71  LPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAPVIGLNDS 130
           +PGDG+++G+G++DGR VFV+A+DFTV+GGSL    A+KI KV   A++ GAP+I LNDS
Sbjct: 72  IPGDGIVSGYGKIDGRQVFVYAYDFTVYGGSLSASNAKKIVKVQQLALKNGAPIIALNDS 131

Query: 131 AGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFTFMVRDTS 190
            GARIQEG++SL G+ +IF +NT ASGV+PQISAI+GPCAGGA YSPALTDF FMV++ S
Sbjct: 132 GGARIQEGIESLSGYADIFYQNTMASGVIPQISAILGPCAGGACYSPALTDFIFMVKEKS 191

Query: 191 HMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHLLSYLPQN 250
           HMF+TGPDV+KTV  EEV+ +ELGGA TH+S SGV HF  +TEE+ L  IR LLS+LPQN
Sbjct: 192 HMFVTGPDVVKTVIHEEVSKEELGGAMTHSSKSGVTHFMCNTEEELLMSIRELLSFLPQN 251

Query: 251 NVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQEDFAKNIV 310
           N+++  +    D+  R    L+ IVP  P  PYD+ D++  V+D G FF V  +FAKNI+
Sbjct: 252 NMDETKKQNCTDETNREDAVLDTIVPADPNVPYDMKDIIERVVDNGYFFEVMTNFAKNII 311

Query: 311 VGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDVPGFLPGT 370
           +GF RL G SVGIVANQP   AG LDI+AS+K +RFIRFCD FNIP+++F DVPGFLPG 
Sbjct: 312 IGFARLAGRSVGIVANQPAYLAGVLDIDASDKASRFIRFCDCFNIPLITFEDVPGFLPGY 371

Query: 371 DQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYAWPTAEIA 430
            QE+NGIIRHGAK++YA++EATVP +TVITRKAYGGAY VM SK  GADVN+A+P+AEIA
Sbjct: 372 TQENNGIIRHGAKIVYAFAEATVPKLTVITRKAYGGAYIVMNSKQTGADVNFAYPSAEIA 431

Query: 431 VMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVIEPGDTRN 490
           VMG +GAVNIL+R       D + +  EL E Y+E+FA PY AA+ GF+D++I P  TR 
Sbjct: 432 VMGAEGAVNILFRKA-----DAETKGKEL-EAYKEKFATPYQAAELGFIDEIIYPRQTRK 485

Query: 491 RLIADLRMLKSKRKSQPDKKHGNIPL 516
           RLI  L M ++K ++ P KKHGN+PL
Sbjct: 486 RLIQALEMTENKMQTNPPKKHGNMPL 511


Lambda     K      H
   0.318    0.138    0.407 

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: 786
Number of extensions: 28
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: 516
Length of database: 511
Length adjustment: 35
Effective length of query: 481
Effective length of database: 476
Effective search space:   228956
Effective search space used:   228956
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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