Alignments for a candidate for pccA in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Rhizobium leguminosarum 3841

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011652112.1 RL_RS13185 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000009265.1:WP_011652112.1
          Length = 673

 Score =  840 bits (2170), Expect = 0.0
 Identities = 439/673 (65%), Positives = 511/673 (75%), Gaps = 9/673 (1%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MFKKILIANRGEIACRVIKTAR+MGI TVAVYSDADR+ALHV MADEA+HIGP  A++SY
Sbjct: 1   MFKKILIANRGEIACRVIKTARRMGILTVAVYSDADRDALHVEMADEAVHIGPAAASESY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +V ++I+ A KA+GAEAVHPGYGFLSER  F   LE  G++FIGP   AI AMGDKI SK
Sbjct: 61  LVAERIIAACKATGAEAVHPGYGFLSERASFCTELEKQGIIFIGPKPKAIMAMGDKIESK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           K A  AGVSTVPG++G+I DA  A  IS  IGYPVMIKASAGGGGKGMRIAW++AEV++G
Sbjct: 121 KFANAAGVSTVPGHLGIIEDAAHAEVISAGIGYPVMIKASAGGGGKGMRIAWNQAEVRDG 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
           FE +++EA +SFGDDR+FIEKFV +PRHIEIQVLAD HGN VYL ERECSIQRRNQKV E
Sbjct: 181 FERARSEAKSSFGDDRVFIEKFVVEPRHIEIQVLADAHGNVVYLGERECSIQRRNQKVAE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSPFLDEATRKAMGEQ+ ALAKAV Y SAGTVEFIVD  +NFYFLEMNTRLQVEHPVT
Sbjct: 241 EAPSPFLDEATRKAMGEQSVALAKAVDYQSAGTVEFIVDRDRNFYFLEMNTRLQVEHPVT 300

Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360
           EL+TGIDLVEQMIRVAAGE LPF Q D++++GWA+ESRLYAEDPYRNFLPSIGRLTRYRP
Sbjct: 301 ELVTGIDLVEQMIRVAAGEPLPFAQEDIRLDGWAVESRLYAEDPYRNFLPSIGRLTRYRP 360

Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420
           P E  T   VVRNDTGV+EG EISMYYDPMIAKLCTWAPTR  AIE M  ALD F V+GI
Sbjct: 361 PAEGRTGNVVVRNDTGVFEGAEISMYYDPMIAKLCTWAPTRLEAIEAMGQALDGFVVDGI 420

Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480
            HN+PF+ A+M HPR+ +G ++T FIAEEYPDGF     D+     +A  A +   +   
Sbjct: 421 EHNVPFLSALMKHPRWREGRLSTGFIAEEYPDGFAPMKPDQAEEAVLAGIALSACLIETN 480

Query: 481 RRTRISGTMNNHERHVGVDWVVALQGESY--------HVSIAADREGSTVSFSDGSSLRV 532
           RR R +  +      +  DWVV + G+++         V+I  D + +     +G S  V
Sbjct: 481 RRERFADRLRAAAGALREDWVVKI-GDNHVAARLLDGLVTIPFDMDIAIEGAIEGESKSV 539

Query: 533 TSDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKL 592
            +DW PG P+    V GR +  ++  +  G R+  +G  +   V +PR AEL  LMP KL
Sbjct: 540 VTDWRPGDPVWRGKVGGRDITAQIRPVLNGLRIDWQGVSVNTKVFSPRHAELDRLMPVKL 599

Query: 593 PPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAP 652
           PPDTSK LLCPMPGLVV I VAEG +V+ G+ LA VEAMKMEN+LRA+R   V KI AA 
Sbjct: 600 PPDTSKLLLCPMPGLVVAIAVAEGQDVKAGETLAIVEAMKMENVLRADRDLVVSKINAAA 659

Query: 653 GASLRVDDVIMEF 665
           G SL VD VIMEF
Sbjct: 660 GESLAVDAVIMEF 672


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: 1203
Number of extensions: 48
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: 666
Length of database: 673
Length adjustment: 39
Effective length of query: 627
Effective length of database: 634
Effective search space:   397518
Effective search space used:   397518
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)
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