Alignments for a candidate for pccA in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Pseudovibrio axinellae Ad2

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_068010793.1 PsAD2_RS22235 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_001623255.1:WP_068010793.1
          Length = 662

 Score =  483 bits (1243), Expect = e-140
 Identities = 285/698 (40%), Positives = 388/698 (55%), Gaps = 57/698 (8%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF KILIANRGEIACR+ K+A+ +GI  VA+YSDAD+ A HVQMADEA  +GPPP  +SY
Sbjct: 1   MFRKILIANRGEIACRIAKSAKALGIKVVAVYSDADRDARHVQMADEAYRLGPPPVAESY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           + +D ++ A + +GA A+HPGYGFLSEN +F EA+EA G++F+GPP  AI AMG K  +K
Sbjct: 61  LNVDALLKAAKHSGADAIHPGYGFLSENPEFVEAVEAAGLVFIGPPADAIRAMGLKDAAK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
            + +++ V  VPGY G  +DA+     S++IGYPV+IKA AGGGGKGMR      +  E 
Sbjct: 121 ALMEKSGVPVVPGYHGANQDAEFLKAESDKIGYPVLIKARAGGGGKGMRRVDAPADFVEA 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
            + ++ E  +SFGD R+ IEK++  PRHIE+QV CD HGN ++L ER+CS+QRR+QKV+E
Sbjct: 181 LEGAQREGQSSFGDPRVLIEKYILSPRHIEVQVFCDGHGNAVHLFERDCSLQRRHQKVIE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQ-----KNFYFLEMNTRLQV 295
           EAP+P + E  R AMG  AV  A+AVGY  AGTVEFIVDG        F+F+EMNTRLQV
Sbjct: 241 EAPAPGMTEEMRAAMGNAAVKAAQAVGYEGAGTVEFIVDGSDGLRADRFWFMEMNTRLQV 300

Query: 296 EHPVTELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRL 355
           EHPVTE ITG DLV     VAAG  L   Q D+ + G + E R+YAED   GFLP+ G L
Sbjct: 301 EHPVTEAITGQDLVNWQFSVAAGGSLPKAQSDLSINGHSFEARIYAEDAEAGFLPATGTL 360

Query: 356 TRYRPPAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPT 415
              + P+  A                     R D+G+  G  I+ +YDPMIAK+ T   T
Sbjct: 361 KELKLPSRFA---------------------RVDSGIRAGDTITPFYDPMIAKVITHGET 399

Query: 416 RAAAIEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLP 475
           R AA+  + +AL+  +  G   N+ FL  +  H  F+ G+M T  I  E     E +   
Sbjct: 400 REAALAKLALALEKSQAVGCTTNITFLHKLATHAGFMKGEMDTGLIDRE----LEKLTTA 455

Query: 476 ETDLRRVAAAAA--------AMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVT 527
            T      A AA        A    A    T    R  +  ++      ++ +G    V+
Sbjct: 456 PTPTNHALALAALIELGFADAPAETASPWDTLTGWRQWSAAKQFAH---LSWRGEPTEVS 512

Query: 528 IAADHDGSTVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRI----RTR 583
               HDGS     +G+S  +      G  L  + +DG  +     +      +     T 
Sbjct: 513 AGRHHDGSLTVSIEGTSFDLRILSNKGQHL-RIDIDGTVITTDFFQSDTSLTLFMGENTW 571

Query: 584 GADLKVHVRTPRQAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTI 643
             DL  H           L  E     +   +  PMPG +  V+   G  V+EG+ L   
Sbjct: 572 HFDLPDH-----------LAEESHEGVSGNAISSPMPGQVRAVNCAAGDTVKEGETLIVT 620

Query: 644 EAMKMENILRAEKKGVVAKINASAGNSLAVDDVIMEFE 681
           EAMKME+ L A + G+VA++ A AG+ +    +++  E
Sbjct: 621 EAMKMEHSLTAPRDGIVAEVMAKAGDQVEEGAILLTLE 658


Lambda     K      H
   0.317    0.134    0.387 

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: 1193
Number of extensions: 52
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 681
Length of database: 662
Length adjustment: 39
Effective length of query: 642
Effective length of database: 623
Effective search space:   399966
Effective search space used:   399966
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)
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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