Alignments for a candidate for pccA in Beijerinckia mobilis UQM 1969

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Beijerinckia mobilis UQM 1969

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_034992903.1 DL88_RS05410 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Dino:3607308
         (681 letters)



>NCBI__GCF_000745425.1:WP_034992903.1
          Length = 668

 Score =  742 bits (1915), Expect = 0.0
 Identities = 394/682 (57%), Positives = 484/682 (70%), Gaps = 17/682 (2%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60
           MFKKILIANRGEIACRVIKTARK+GI TVA++S+ADRNALHVRMADEAV IG + A++SY
Sbjct: 1   MFKKILIANRGEIACRVIKTARKLGISTVAVFSEADRNALHVRMADEAVFIGAAAASESY 60

Query: 61  IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120
           +V+DK++ A  +TGAEAVHPGYGFLSE   F EAL  +G+ FIGP A AIEAMGDKI SK
Sbjct: 61  LVMDKIVAACVETGAEAVHPGYGFLSERAAFPEALAAKGIVFIGPNAKAIEAMGDKIQSK 120

Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180
           K AQ A VS VPG++G I   ++A +I+ +IGYPVMIKASAGGGGKGMRIA +  EA EG
Sbjct: 121 KYAQAAGVSVVPGFLGEIETPEDAARIADDIGYPVMIKASAGGGGKGMRIAHSREEAIEG 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
           F  +++EA +SFGDDR+FIEKF+ +PRHIEIQVL D HGN I+LGERECSIQRRNQKV+E
Sbjct: 181 FARARSEAKSSFGDDRVFIEKFIIEPRHIEIQVLGDKHGNIIHLGERECSIQRRNQKVIE 240

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300
           EAPSP LD ATR+ MG ++ ALA+AVGY SAGTVEF+   D+ FYFLEMNTRLQVEHPVT
Sbjct: 241 EAPSPLLDAATREKMGAEAVALAKAVGYDSAGTVEFVAGQDKQFYFLEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360
           EL+TG+DLVEQMIR+AAGEKL +TQ DVTL GWA+E+R+YAEDP RNFLPS GRL  YRP
Sbjct: 301 ELVTGLDLVEQMIRIAAGEKLTLTQHDVTLRGWAVESRVYAEDPARNFLPSTGRLVTYRP 360

Query: 361 PVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAI 420
           P E     +                +RNDTGVYEG EIS+ YDPMIAK  T+G  R AA+
Sbjct: 361 PAEGLVDGI---------------TIRNDTGVYEGAEISINYDPMIAKFITYGGSRQAAV 405

Query: 421 EAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLT 480
           EA   ALD F + GI HN+PF+ +VM H  F  G+++T F+ E+YP GF        +  
Sbjct: 406 EAQAEALDAFVIHGIRHNIPFLNSVMRHERFRSGKLSTQFLAEEYPKGFTPHVPQGEEAL 465

Query: 481 RLAAAAAAMFRVAEIRRTRISGTLDNHERMVGT-DWVVTAQDARFDVTIDADPGGSTVRF 539
            LAA AAA+  V   R+  I+  L   + +  T +  V     R+D+ I+    G+ V F
Sbjct: 466 ALAAVAAAIDDVLNERKRHITTQLPAAKPVTFTKERSVLLGKERYDIRIEHGVEGARVHF 525

Query: 540 -ADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVRTPRQAE 598
             +   +   S W  G+ +    I+G    ++V  I +GF +   GA+V+  V T R+A+
Sbjct: 526 EKENLFYFCRSSWRGGEIVWHGTINGVAACVQVQPIPNGFCLARGGAEVEARVYTRREAD 585

Query: 599 LNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTA 658
           L+  MPEK   + SK LLCPMPGLV  I V  G EV+ G  LC VEAMKMEN+LRA++  
Sbjct: 586 LSAFMPEKAQAEASKALLCPMPGLVRAIHVAPGQEVKAGDPLCVVEAMKMENVLRADQDV 645

Query: 659 TVTKINAGAGDSLAVDDVIMEF 680
           T+  + A  GDSLAVD VIMEF
Sbjct: 646 TIKSVLAKEGDSLAVDAVIMEF 667


Lambda     K      H
   0.318    0.134    0.392 

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: 1215
Number of extensions: 48
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: 681
Length of database: 668
Length adjustment: 39
Effective length of query: 642
Effective length of database: 629
Effective search space:   403818
Effective search space used:   403818
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: 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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Steps (tab-delimited)
Rules (tab-delimited)
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 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