Alignments for a candidate for pccB in Desulfatiglans anilini DSM 4660

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Desulfatiglans anilini DSM 4660

Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_051185093.1 H567_RS0117950 acyl-CoA carboxylase subunit beta

Query= SwissProt::I3R7F1
         (516 letters)



>NCBI__GCF_000422285.1:WP_051185093.1
          Length = 528

 Score =  478 bits (1231), Expect = e-139
 Identities = 232/515 (45%), Positives = 331/515 (64%), Gaps = 4/515 (0%)

Query: 4   EDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHK 63
           + R+++  ++RE+ ++ GG   +     KG MTARER+DYF D GTF E   F THR   
Sbjct: 12  QKRMEDWWQRREKIMQMGGPKAVEQHRKKGLMTARERVDYFFDAGTFTEIGTFVTHRATA 71

Query: 64  FGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAP 123
           FGM+  ++P DGV+TG G V+GR V   + D+T  GGS GE    K    +D A + G P
Sbjct: 72  FGMDNKEVPADGVVTGFGTVNGRYVVTASEDYTCMGGSFGEAHGRKFAYAIDFAKDKGWP 131

Query: 124 VIGLNDSAGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFT 183
            + +NDS G R+QEG+ +L  +G +FR   +ASG++PQIS I+GPC GG  Y P + DF 
Sbjct: 132 FVSMNDSGGLRMQEGMDALEAYGWLFRAQDQASGIIPQISLILGPCLGGQAYHPVMQDFV 191

Query: 184 FMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHL 243
             VR +  + I GP  +K  T EE++ ++L G   H   SG  H   + ++  LD  + L
Sbjct: 192 IQVRGSGFLGIAGPAFVKAQTAEEISLEDLCGVKAHAVKSGQTHIVAENDKDCLDKCKQL 251

Query: 244 LSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQE 303
           LS+ P NN E PP V   D+PER  + L +I+PD+P + +D++ ++  V+DE SFF    
Sbjct: 252 LSFFPSNNKEAPPTVVSKDNPEREIEGLLDIIPDEPFRVFDMYKIIKKVVDEDSFFETLS 311

Query: 304 DFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDV 363
            +A N++ GF R +G +VGIVANQP   AG +DI AS+K ARFIRFCD FNIP+++FVD 
Sbjct: 312 QYATNMITGFARFNGRTVGIVANQPCRLAGAIDINASDKAARFIRFCDLFNIPLITFVDC 371

Query: 364 PGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYA 423
           P ++ G+ Q+  GI+RHGAKLL+A+S ATVPL+++I RK+Y GA+  M  K +GAD  YA
Sbjct: 372 PAYMIGSQQDWGGILRHGAKLLFAWSNATVPLISIIIRKSYAGAHYGMLDKSIGADFVYA 431

Query: 424 WPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVI 483
           WPTA +  +  +   ++++  E++AADD +  R + I EY E +ANPY AA RGF+DDVI
Sbjct: 432 WPTAIVTALDGKTVASVIFDKEIKAADDSEKIRAQKIAEYNEIYANPYHAAARGFIDDVI 491

Query: 484 EPGDTRNRLIADLRMLKSKRK----SQPDKKHGNI 514
           +P DTR  +   L +L++K K    SQP +K+ NI
Sbjct: 492 DPKDTRKIINNSLNVLQNKWKTSYYSQPWRKYSNI 526


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: 700
Number of extensions: 27
Number of successful extensions: 1
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: 528
Length adjustment: 35
Effective length of query: 481
Effective length of database: 493
Effective search space:   237133
Effective search space used:   237133
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)
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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