Alignments for a candidate for pccA in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Xanthobacter autotrophicus Py2

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012113878.1 XAUT_RS09310 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000017645.1:WP_012113878.1
          Length = 666

 Score =  529 bits (1363), Expect = e-154
 Identities = 309/668 (46%), Positives = 402/668 (60%), Gaps = 39/668 (5%)

Query: 3   KKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYIV 62
           + +L+ANRGEIA RV++TA+ MGI+TVAVYS AD NALHV+ ADEA  IGP PA +SY+ 
Sbjct: 6   RTLLVANRGEIAVRVMRTAKAMGIRTVAVYSQADANALHVASADEAYPIGPAPARESYLR 65

Query: 63  IDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKKL 122
           ID I++A + SGA+A+HPGYGFLSE   FA A E AG+VF+GPP+ AI AMG K  +K L
Sbjct: 66  IDAILDAARKSGADAIHPGYGFLSENAAFAEACEKAGIVFVGPPASAIRAMGSKSAAKAL 125

Query: 123 AKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGFE 182
            ++AGV  VPGY G   DA    + +  IG+PV+IKASAGGGGKGM++  S AE  +   
Sbjct: 126 MEKAGVPLVPGYHGEDQDAGLLAREAERIGFPVLIKASAGGGGKGMKVVRSAAEFPDALA 185

Query: 183 SSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEEA 242
           S++ EA ++FGDDR+ +EK++T PRHIE+QV AD HGN VYLHER+CSIQRR+QKV+EEA
Sbjct: 186 SAQREAKSAFGDDRVLVEKYLTTPRHIEVQVFADSHGNAVYLHERDCSIQRRHQKVVEEA 245

Query: 243 PSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTEL 302
           P+P +    R AMG+ A   AKAVGY  AGTVEFI + + NFYF+EMNTRLQVEHPVTE 
Sbjct: 246 PAPGMTPERRAAMGKAAVDAAKAVGYVGAGTVEFIAESE-NFYFMEMNTRLQVEHPVTES 304

Query: 303 ITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRPPV 362
           ITG DLVE  I+VA GEKLP  Q+D+ ++G A+E RLYAEDP R+FLP +GRL     P 
Sbjct: 305 ITGQDLVEWQIKVAQGEKLPLAQADIPLHGHAIEVRLYAEDPARDFLPQVGRLDHLVLPF 364

Query: 363 ESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGIGH 422
                 +  R DTGV  G  +S++YDPMIAK+      R  A+  +  AL   EV G+  
Sbjct: 365 H----LNGTRVDTGVRAGDTVSIHYDPMIAKIIVSGADRTEAVRRLDAALAATEVVGLAT 420

Query: 423 NLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVL--DEPTLRRVAAAAAAMNRVAEI 480
           N  F+ A+  HP F   ++ T FIA       Q  +L   EP    V A AA      E 
Sbjct: 421 NRVFLKAIATHPAFAAAELDTNFIARH-----QDLLLPPPEPVDDTVLALAALFVLKEEA 475

Query: 481 RRTR--------------ISGTMNNHERHVGVDWVVALQGESYHVSIAAD-REGSTVSFS 525
           R++                 G   N + HV + +          +++ A  R    +   
Sbjct: 476 RQSAEAVDAADPWSPWGLAPGWRLNRDAHVDLTFA----DRDRRIAVRAHFRPSGFILSL 531

Query: 526 DGSSLRVTSDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELA 585
            G  + V  D      L +  +DG  L  +V +      + +RG +  +    PR A  A
Sbjct: 532 PGGDMSVEGDAEADGTLRA-RLDGVALSARVIRTAAHLTVFVRGGEYGLEFIDPRLASQA 590

Query: 586 LLMPEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTV 645
                     T+  L+ PMPG +++I V EG EV EG AL  VEAMKME+ + A R G V
Sbjct: 591 -------ATGTAGRLVAPMPGTIIRIAVEEGQEVAEGAALVVVEAMKMEHTVAAPRDGKV 643

Query: 646 KKIAAAPG 653
           K +  A G
Sbjct: 644 KTLKFAVG 651


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: 1093
Number of extensions: 47
Number of successful extensions: 4
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: 666
Length adjustment: 38
Effective length of query: 628
Effective length of database: 628
Effective search space:   394384
Effective search space used:   394384
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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 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