Alignments for a candidate for pccA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Acidovorax sp. GW101-3H11

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_3016 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

Query= metacyc::MONOMER-13589
         (666 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3016
          Length = 675

 Score =  507 bits (1306), Expect = e-148
 Identities = 300/665 (45%), Positives = 388/665 (58%), Gaps = 20/665 (3%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MFKKILIANRGEIACRV  TA+++G++TVAVYSDAD NA HV++ DEA+HIG      SY
Sbjct: 1   MFKKILIANRGEIACRVAATAQRLGVKTVAVYSDADANAKHVAVCDEAVHIGGSAPKDSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +  ++I+EA KA+GA+A+HPGYGFLSE  DFA A  AAG+VFIGPP+ AI+ MG K  SK
Sbjct: 61  LRWERIIEAAKATGAQAIHPGYGFLSENEDFAQACAAAGLVFIGPPASAIKDMGLKAESK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           +L ++AGV  VPGY G   D     + ++ IGYPV+IKASAGGGGKGMR      +    
Sbjct: 121 QLMEKAGVPLVPGYHGSDQDPALLQREADRIGYPVLIKASAGGGGKGMRAVDKSEDFAAA 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
            ES K EA NSFGDD + +EK+V +PRHIEIQV  D HGNCVYL ER+CS+QRR+QKV+E
Sbjct: 181 LESCKREAINSFGDDAVLVEKYVQRPRHIEIQVFGDMHGNCVYLFERDCSVQRRHQKVLE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVD--------GQKNFYFLEMNTR 292
           EAP+P +  A R  MGE A A AKAV Y  AGTVEFIV+         Q  FYF+EMNTR
Sbjct: 241 EAPAPGMTPALRAQMGEAAVAAAKAVNYVGAGTVEFIVEQPGGYERPDQMKFYFMEMNTR 300

Query: 293 LQVEHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSI 352
           LQVEHPVTE ITG+DLVE  +RVA+GE LP QQ DL+I G A+E+R+ AE+P  NFLP+ 
Sbjct: 301 LQVEHPVTEAITGLDLVEWQLRVASGEPLPLQQQDLRITGHAIEARICAENPDNNFLPAT 360

Query: 353 GRLTRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLAL 412
           G L  Y  P         +R D+GV +G  IS +YD M+AKL     TRE A+  +  AL
Sbjct: 361 GALNVYALPECVTFERGAIRVDSGVRQGDAISPFYDSMVAKLIVHGDTREQALARLDDAL 420

Query: 413 DTFEVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAA 472
               + G+  N+ F+  V     F +  + TA I  E    F      EP    +AAAAA
Sbjct: 421 AQTHIVGLATNVQFLRRVAKTDAFAQAKLDTALIPREQAVLFH----QEPVGLPLAAAAA 476

Query: 473 AMNRVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRV 532
                  + + R S  ++   R  G      +Q   +      +   + +++  G SL +
Sbjct: 477 V---AQTLLKERASEGVDPFSRRDGFHTHGVVQ-RRFEFEFGGEHAKALLTYERGGSLHL 532

Query: 533 T----SDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLM 588
                     G  + +   DG  L     +       +     +   +   +   + LL 
Sbjct: 533 AVGEGETAVAGPLVFAPQADGIELQFAGQRTRAAVYAQGEVDHVFTPLGATQITAIDLLA 592

Query: 589 PEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKI 648
                      L  PMPG VV   V  GD V +GQ LA +EAMKME+ + A   G V+++
Sbjct: 593 HAGEVAAEGGRLTAPMPGKVVSFAVKAGDTVAKGQPLAVMEAMKMEHTIAAPADGVVQEL 652

Query: 649 AAAPG 653
             APG
Sbjct: 653 LYAPG 657


Lambda     K      H
   0.318    0.134    0.386 

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: 1120
Number of extensions: 49
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 2
Length of query: 666
Length of database: 675
Length adjustment: 39
Effective length of query: 627
Effective length of database: 636
Effective search space:   398772
Effective search space used:   398772
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 17 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