Alignments for a candidate for pccA in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Pseudomonas litoralis 2SM5

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_090274990.1 BLU11_RS15720 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_900105005.1:WP_090274990.1
          Length = 640

 Score =  480 bits (1236), Expect = e-140
 Identities = 283/668 (42%), Positives = 382/668 (57%), Gaps = 47/668 (7%)

Query: 5   ILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYIVID 64
           +L+ANRGEIACRV+ TA+ MG+ TVAV+S  D NA H   AD  I +G      SY+ ID
Sbjct: 8   LLVANRGEIACRVMSTAKSMGLTTVAVHSAVDANARHAREADIRIDLGGAKPADSYLQID 67

Query: 65  KIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKKLAK 124
           K++ A K+SGA+A+HPGYGFLSE   FA A+EAAG++F+GPP+ AI+AMG K  +K L +
Sbjct: 68  KLIAAAKSSGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPAAAIDAMGSKSAAKALME 127

Query: 125 EAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGFESS 184
           EAGV  VPGY G   D +     +  IGYPV++KA+AGGGGKGM++   E ++ E   S+
Sbjct: 128 EAGVPLVPGYHGEAQDLETFRAAAELIGYPVLLKATAGGGGKGMKVVEREEDLAEALASA 187

Query: 185 KNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEEAPS 244
           + EA +SFGD R+ +EK+V +PRH+EIQ+ AD+ GNC+YL+ER+CSIQRR+QKV+EEAP+
Sbjct: 188 QREAQSSFGDARMLVEKYVLKPRHVEIQIFADQQGNCLYLNERDCSIQRRHQKVVEEAPA 247

Query: 245 PFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTELIT 304
           P L    R+AMGE A   A+A+GY  AGTVEF++D +  F+F+EMNTRLQVEHPVTE IT
Sbjct: 248 PGLSAELRRAMGEAAVTAARAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 307

Query: 305 GIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRPPVES 364
           G+DLV   IRVA GE LP  Q  + + G A+E RLYAEDP  +FLPS G L  YR   E+
Sbjct: 308 GLDLVAWQIRVARGEPLPITQEQVPLIGHAIEVRLYAEDPDNDFLPSTGTLALYR---EA 364

Query: 365 VTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGIGHNL 424
            T     R D+GV EG  +S +YDPM+ KL  W   RE A   +   LD   + G+  NL
Sbjct: 365 ATGAG-RRVDSGVAEGDSVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAIGGVRTNL 423

Query: 425 PFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEIRRTR 484
            F+  V+ HP F   ++ T FI     D  + A     T  + AA A         R   
Sbjct: 424 AFLRRVVGHPAFADAELDTDFIPRHETDLLRPASKLSDTFWQQAAEAFVSTTPVVARSDD 483

Query: 485 ISGTMNNHE-RHVGVDWVVAL----QGESYHVSIAADREGSTVSFSDGSSLRVTSDWTPG 539
                + ++   +G+   + L     GES  V +                   TS  +  
Sbjct: 484 AHSPWSRYDGLRLGMPAQITLHLQCNGESRRVQL------------------TTSQPSSS 525

Query: 540 QPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTP-RQAELALLMPEKLPPDTSK 598
           +PL   +     L            L+  G  L V    P  +A+ +L            
Sbjct: 526 EPLPRAIRQNDTLY-----------LQHSGEWLAVTAFDPITEAQDSL--------QQQG 566

Query: 599 YLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGASLRV 658
            L  PM G +V++ V  G  V  G AL  +EAMKME+ +R+ + G VK +    G  +  
Sbjct: 567 GLTAPMNGSIVRVLVEAGQHVAAGTALIVLEAMKMEHSIRSAQDGVVKSLFCNEGDMVSE 626

Query: 659 DDVIMEFE 666
             V++E E
Sbjct: 627 GTVLLELE 634


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: 996
Number of extensions: 45
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 666
Length of database: 640
Length adjustment: 38
Effective length of query: 628
Effective length of database: 602
Effective search space:   378056
Effective search space used:   378056
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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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 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