Alignments for a candidate for pccA in Dechloromonas agitata is5

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Dechloromonas agitata is5

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_027457190.1 K420_RS0105525 acetyl-CoA carboxylase biotin carboxylase subunit

Query= reanno::PS:Dsui_0516
         (663 letters)



>NCBI__GCF_000519045.1:WP_027457190.1
          Length = 667

 Score = 1191 bits (3082), Expect = 0.0
 Identities = 600/667 (89%), Positives = 622/667 (93%), Gaps = 4/667 (0%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MFKKILIANRGEIACRVIKTARKMGI TVAVYSEADKDAL V++ADEAVCIGPAASKESY
Sbjct: 1   MFKKILIANRGEIACRVIKTARKMGIATVAVYSEADKDALHVDLADEAVCIGPAASKESY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           LV DKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYS+AKMGDKIESK
Sbjct: 61  LVMDKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSVAKMGDKIESK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
           KLAIEAKVNTIPGYNDAI GP  AVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEA EG
Sbjct: 121 KLAIEAKVNTIPGYNDAIAGPAEAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAFEG 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
           FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE
Sbjct: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300
           EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV
Sbjct: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300

Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360
           TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ
Sbjct: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
           PP E+ GQVRVDTGVYDGGEISM+YDSMIAKLIVHGA+REQAIARMRDALNGFVIRGISS
Sbjct: 361 PPKEIPGQVRVDTGVYDGGEISMFYDSMIAKLIVHGATREQAIARMRDALNGFVIRGISS 420

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480
           NIPFQAALMQH  F SGIFDTGFI K YP GFDASMVPHDDPALL+ VAA+V+R Y DR+
Sbjct: 421 NIPFQAALMQHPVFHSGIFDTGFIPKHYPTGFDASMVPHDDPALLVSVAAYVYRAYTDRS 480

Query: 481 AQVSGQLPGHERKVGDEWVVIR----NGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQG 536
           A VSGQL GHER VGD+W+V+R      E H V A+PI GGY V Y GE+YE+LSDW+ G
Sbjct: 481 ASVSGQLQGHERIVGDQWMVVRLNKEGNEHHEVTARPIPGGYHVEYKGEQYEILSDWKLG 540

Query: 537 QSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKF 596
           +SLFNGTCNGEEFTLQVERH+  Y LFHWGTRAD MVMSARAAELLALMPEK APDLSKF
Sbjct: 541 ESLFNGTCNGEEFTLQVERHKTKYSLFHWGTRADFMVMSARAAELLALMPEKPAPDLSKF 600

Query: 597 LLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVD 656
           LLSPMPGLLRE++V VGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKIS   G SLSVD
Sbjct: 601 LLSPMPGLLREIAVQVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISAAVGESLSVD 660

Query: 657 EIIIEFE 663
           +IIIEFE
Sbjct: 661 QIIIEFE 667


Lambda     K      H
   0.319    0.135    0.391 

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: 1462
Number of extensions: 36
Number of successful extensions: 2
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: 663
Length of database: 667
Length adjustment: 38
Effective length of query: 625
Effective length of database: 629
Effective search space:   393125
Effective search space used:   393125
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 (21.7 bits)
S2: 54 (25.4 bits)

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

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Candidates (tab-delimited)
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