Alignments for a candidate for pccA in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Rhizorhabdus wittichii RW1

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012049091.1 SWIT_RS14620 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000016765.1:WP_012049091.1
          Length = 660

 Score =  818 bits (2112), Expect = 0.0
 Identities = 426/670 (63%), Positives = 501/670 (74%), Gaps = 14/670 (2%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MFKKILIANRGEIACRVIKTAR+MGI+TVAVYSDAD  A HV MADEA+HIG  PA++SY
Sbjct: 1   MFKKILIANRGEIACRVIKTARRMGIKTVAVYSDADARAPHVEMADEAVHIGASPASESY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           ++ D+I++A K +GAEAVHPGYGFLSER  FA AL AA + FIGPP+ AI AMGDKI SK
Sbjct: 61  LIADRIIQACKDTGAEAVHPGYGFLSERTSFAEALAAANIAFIGPPANAIAAMGDKIESK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           KLA EAGV+ VPGY+G I D D AV+I+N+IGYPVM+KASAGGGGKGMR+A+SE +V+E 
Sbjct: 121 KLAMEAGVNVVPGYVGEIDDTDHAVRIANDIGYPVMMKASAGGGGKGMRLAYSEKDVREN 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
           F+S K E  NSFGDDR+FIEKF+  PRHIEIQVL DKHGN VYL+ERECSIQRR+QKV+E
Sbjct: 181 FDSVKREGLNSFGDDRVFIEKFIESPRHIEIQVLGDKHGNIVYLNERECSIQRRHQKVVE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQ----KNFYFLEMNTRLQVE 296
           EAPSPF+    RKAMGEQ  ALA+AVGY SAGTVE IV G     + FYFLEMNTRLQVE
Sbjct: 241 EAPSPFVSPEMRKAMGEQCVALARAVGYFSAGTVELIVSGADKTGQGFYFLEMNTRLQVE 300

Query: 297 HPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLT 356
           HPVTE ITG+DLVEQMIRVA GEKL F Q+D+KINGWA+E+R+YAEDPYR FLPS GRL 
Sbjct: 301 HPVTECITGLDLVEQMIRVAYGEKLAFTQADVKINGWAVENRVYAEDPYRGFLPSTGRLV 360

Query: 357 RYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFE 416
           RYRPP E       VR D GVYEG EISM+YDPMIAKL TW  TREAAI+    ALD FE
Sbjct: 361 RYRPPAE----VDNVRVDDGVYEGSEISMFYDPMIAKLITWGETREAAIDRQITALDRFE 416

Query: 417 VEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNR 476
           ++GIGHN+ F+ A+M HPRF  G+ITT FIAEE+P+GF GA  D      +AA A  +  
Sbjct: 417 IDGIGHNVDFLSALMQHPRFRSGNITTGFIAEEFPEGFTGAAADAKLGLHLAAVAGVLAS 476

Query: 477 VAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSDW 536
           +   R  +I G +N         WVV L      + I     G  VS  DG+ + V + +
Sbjct: 477 IDTARAAQIDGRLNG-PADPSTSWVVTLDKVERQIEIL----GDAVSV-DGTPVVVDAPY 530

Query: 537 TPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPDT 596
            PGQ L   ++DG PL ++V +   G+R   RGA  ++ V TPR A LA  M EK+PPD 
Sbjct: 531 VPGQKLVEAVIDGEPLSIRVERKRTGWRFTTRGASHELRVLTPRVASLAHHMIEKIPPDM 590

Query: 597 SKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGASL 656
           S++LLCPMPGLV  I+VAEG +V+ GQ LA VEAMKMENILRAE+ GTVK +AA  G SL
Sbjct: 591 SRFLLCPMPGLVTAIHVAEGAKVEAGQPLAVVEAMKMENILRAEKAGTVKAVAAKAGDSL 650

Query: 657 RVDDVIMEFE 666
            VD VI+EFE
Sbjct: 651 AVDAVILEFE 660


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: 1157
Number of extensions: 46
Number of successful extensions: 5
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: 660
Length adjustment: 38
Effective length of query: 628
Effective length of database: 622
Effective search space:   390616
Effective search space used:   390616
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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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