Aligments for a candidate for pccA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Aligments for a candidate for pccA in Pseudomonas fluorescens FW300-N2E3

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate AO353_19305 AO353_19305 3-methylcrotonyl-CoA carboxylase

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



>FitnessBrowser__pseudo3_N2E3:AO353_19305
          Length = 653

 Score =  492 bits (1266), Expect = e-143
 Identities = 278/671 (41%), Positives = 398/671 (59%), Gaps = 29/671 (4%)

Query: 3   KKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYIV 62
           +KILIANRGEIACR+ +TA+ +G +TVAV+SDAD +ALHV MADEA++IGP    QSY+ 
Sbjct: 5   RKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVRMADEAVNIGPAAVAQSYLN 64

Query: 63  IDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKKL 122
              I++A   SGA+A+HPGYGFLSE  +FA A   AG+ FIGP   AIE MG K  SK  
Sbjct: 65  SAAIIDAALRSGADAIHPGYGFLSENAEFATACAQAGITFIGPDPAAIELMGSKRLSKIA 124

Query: 123 AKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGFE 182
              AGV  + GY G   D     + +  IGYP+MIKASAGGGG+GMR+  +  E+     
Sbjct: 125 MLAAGVPCIGGYQGAEQDDATLSREAERIGYPLMIKASAGGGGRGMRLVHTADELLAQIR 184

Query: 183 SSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEEA 242
           ++++EA ++FG D + +E+ + +PRH+EIQ+  D+HGN +YL ER+CSIQRR+QKVIEEA
Sbjct: 185 TARSEALHAFGSDELILEQALIEPRHVEIQLFGDQHGNLIYLGERDCSIQRRHQKVIEEA 244

Query: 243 PSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTEL 302
           P P +    R AMGE A    +AV Y  AGTVEF++D +  FYFLEMNTRLQVEHPVTE+
Sbjct: 245 PCPVMTAELRDAMGEAALKAGRAVNYVGAGTVEFLLDARGQFYFLEMNTRLQVEHPVTEM 304

Query: 303 ITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRPPV 362
           ITG+DLV   + VAAG  LP +Q  +++ G AME RLYAEDP ++FLP  GR+ R+ P +
Sbjct: 305 ITGLDLVAWQLDVAAGLPLPLRQEQVELKGHAMEVRLYAEDPAQDFLPQTGRIMRWEPAL 364

Query: 363 ESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGIGH 422
                   VR D G+ EG ++S +YDP++ K+  +  TRE A  ++  A+    + G+  
Sbjct: 365 -----ADGVRIDHGLLEGQQVSPFYDPLLGKIIAYGATREEARRKLLRAVQDSALLGLQT 419

Query: 423 NLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAM-NRVAEIR 481
           N   +  +++HP+F+ GD  T FIA+ + D         PT   +A A A    + A   
Sbjct: 420 NQRLLAGLLEHPQFIAGDFNTGFIAQHFAD-HPSLHSHAPTAEELAIATALFYQQSAGAH 478

Query: 482 RTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSDWTPGQP 541
              ++G  NN   +  +   + L G+ +   + A  +G  V    G +L+          
Sbjct: 479 PPGLAGWRNN--ANAPLLQQIGLNGDRWSTEVTALPDGQLVIQVAGETLQ---------- 526

Query: 542 LASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPDTSKY-- 599
           L  L ++ R   +++  I   +  +L    L +  R        LL  + L P +S+   
Sbjct: 527 LKLLDINARSANLEINGIRRRYAYQLAAGQLWLFTRPGS----LLLQDQTLAPVSSQVGT 582

Query: 600 ----LLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGAS 655
               L  PM G +V + V+EG  V +GQ L  +EAMKME+ L+A   G +K++  +PG  
Sbjct: 583 STGTLKAPMDGAIVDVLVSEGSSVTKGQLLLVLEAMKMEHPLKAGIDGVIKRLQVSPGDQ 642

Query: 656 LRVDDVIMEFE 666
           ++   +++E E
Sbjct: 643 VKNRQILLEVE 653


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: 1001
Number of extensions: 40
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: 666
Length of database: 653
Length adjustment: 38
Effective length of query: 628
Effective length of database: 615
Effective search space:   386220
Effective search space used:   386220
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, or view the source code.

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