Alignments for a candidate for pccA in Azoarcus sp. BH72

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Azoarcus sp. BH72

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_011764423.1 AZO_RS03455 acetyl-CoA carboxylase biotin carboxylase subunit

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



>NCBI__GCF_000061505.1:WP_011764423.1
          Length = 668

 Score = 1155 bits (2989), Expect = 0.0
 Identities = 583/668 (87%), Positives = 618/668 (92%), Gaps = 5/668 (0%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MF KILIANRGEIACRVIKTARKMGIKTVAVYSEADKDAL V++ADEAVCIGPA SK+SY
Sbjct: 1   MFTKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALHVDLADEAVCIGPAPSKDSY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           LV D+IIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYS+AKMGDKIESK
Sbjct: 61  LVMDRIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSVAKMGDKIESK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
           KLAIEAKVNTIPGYNDAI GP  AVEIAKKIGYPVMIKASAGGGGKGLRVAYND +A EG
Sbjct: 121 KLAIEAKVNTIPGYNDAIAGPAEAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDEQAFEG 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
           FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE
Sbjct: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300
           EAPSPFVD EMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV
Sbjct: 241 EAPSPFVDAEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300

Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360
           TELITGLDLVEQMIRVA GEKLPL+QADV+INGWAMECRINAEDPFRGFLPSTGRLV+FQ
Sbjct: 301 TELITGLDLVEQMIRVAAGEKLPLSQADVKINGWAMECRINAEDPFRGFLPSTGRLVRFQ 360

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
           PPAEVDGQVRVDTGVYDGGEISM+YDSMIAKLIVHGA+R+QAI RMRDALN FVIRGISS
Sbjct: 361 PPAEVDGQVRVDTGVYDGGEISMFYDSMIAKLIVHGATRDQAIGRMRDALNAFVIRGISS 420

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480
           NIPFQAALMQH RF SG F+TGFIA+E+PKGFDASMVPHDDPALL  VAA+VHR YIDRA
Sbjct: 421 NIPFQAALMQHPRFCSGNFNTGFIAEEFPKGFDASMVPHDDPALLAAVAAYVHRSYIDRA 480

Query: 481 AQVSGQLPGHERKVGDEWVVIRNG-----ERHPVVAKPIEGGYLVTYNGEKYELLSDWRQ 535
           A+VSGQLPGHER VG+EWVVIR G     E  PV A P+ GGY VT NGE Y + SDW+ 
Sbjct: 481 ARVSGQLPGHERAVGNEWVVIRLGTDNQNELLPVTATPVAGGYAVTLNGETYTIKSDWQL 540

Query: 536 GQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSK 595
           GQ+LFNGTCNG EFTLQVERH+M Y+LFHWGT+AD +VMS RAAEL +LMP K  PDLSK
Sbjct: 541 GQALFNGTCNGNEFTLQVERHKMRYRLFHWGTQADFLVMSKRAAELQSLMPVKLPPDLSK 600

Query: 596 FLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSV 655
           FLLSPMPGLLREVSV+ GQEVKAGEKLAVIEAMKMEN+LKAEQD KVKK+ +  G+SL+V
Sbjct: 601 FLLSPMPGLLREVSVSEGQEVKAGEKLAVIEAMKMENLLKAEQDGKVKKVVIKPGASLAV 660

Query: 656 DEIIIEFE 663
           D++IIEFE
Sbjct: 661 DDVIIEFE 668


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: 1393
Number of extensions: 45
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: 668
Length adjustment: 38
Effective length of query: 625
Effective length of database: 630
Effective search space:   393750
Effective search space used:   393750
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 Sep 24 2021. 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)
SQLite3 databases

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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 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