Alignments for a candidate for liuB in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Pseudovibrio axinellae Ad2

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_068010793.1 PsAD2_RS22235 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Smeli:SM_b21124
         (662 letters)



>NCBI__GCF_001623255.1:WP_068010793.1
          Length = 662

 Score =  716 bits (1849), Expect = 0.0
 Identities = 378/665 (56%), Positives = 461/665 (69%), Gaps = 7/665 (1%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           MF K+LIANRGEIACRI ++A+ LGI+ VAVYSDAD DA HV +ADEA R+G  P AESY
Sbjct: 1   MFRKILIANRGEIACRIAKSAKALGIKVVAVYSDADRDARHVQMADEAYRLGPPPVAESY 60

Query: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120
           L    +++AA+  GA AIHPGYGFLSEN +F EAV  AG++F+GPP  AIRAMGLKDAAK
Sbjct: 61  LNVDALLKAAKHSGADAIHPGYGFLSENPEFVEAVEAAGLVFIGPPADAIRAMGLKDAAK 120

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
           ALME+SGVPVVPGYHG  QDA FL   + +IGYPVLIKARAGGGGKGMRRV+   DF  A
Sbjct: 121 ALMEKSGVPVVPGYHGANQDAEFLKAESDKIGYPVLIKARAGGGGKGMRRVDAPADFVEA 180

Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240
           LE A+RE +S+FGD  VL+E+Y+  PRHIE+QVF D HGN VHLFERDCSLQRRHQKVIE
Sbjct: 181 LEGAQREGQSSFGDPRVLIEKYILSPRHIEVQVFCDGHGNAVHLFERDCSLQRRHQKVIE 240

Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300
           EAPAPGMT E+R AMG+AAV+AAQA+GY GAGTVEFI D ++GL  D F+FMEMNTRLQV
Sbjct: 241 EAPAPGMTEEMRAAMGNAAVKAAQAVGYEGAGTVEFIVDGSDGLRADRFWFMEMNTRLQV 300

Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360
           EHPVTEAITG DLV WQ  VA+G  LPK Q+D+S+NG +FEAR+YAED   GFLPATG L
Sbjct: 301 EHPVTEAITGQDLVNWQFSVAAGGSLPKAQSDLSINGHSFEARIYAEDAEAGFLPATGTL 360

Query: 361 TELSFPEGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTV 420
            EL  P   +RVDSG+R GDTITP+YDP+IAK+I HG+ R AAL +L  AL++ +  G  
Sbjct: 361 KELKLPSRFARVDSGIRAGDTITPFYDPMIAKVITHGETREAALAKLALALEKSQAVGCT 420

Query: 421 TNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEALALAAIFSTGALD-PNRS 479
           TN  FL +L     F  G  DTGLIDRE+E+LT    P + ALALAA+   G  D P  +
Sbjct: 421 TNITFLHKLATHAGFMKGEMDTGLIDRELEKLTTAPTPTNHALALAALIELGFADAPAET 480

Query: 480 TDPWSSLGSWQIWGDAHRMVVIEHADVRATVTLASRGR---DQFAVRAGASTLPVLVLDR 536
             PW +L  W+ W  A +     H   R   T  S GR       V    ++  + +L  
Sbjct: 481 ASPWDTLTGWRQWSAAKQFA---HLSWRGEPTEVSAGRHHDGSLTVSIEGTSFDLRILSN 537

Query: 537 FEGGARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDELVAPMP 596
                R+++ G      F +   +LTLF G     F +PD L       ++ + + +PMP
Sbjct: 538 KGQHLRIDIDGTVITTDFFQSDTSLTLFMGENTWHFDLPDHLAEESHEGVSGNAISSPMP 597

Query: 597 GLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEGTVLVTL 656
           G V+ V   AGD V +G+ L+V EAMKME +L+A R+G +A V    G QV EG +L+TL
Sbjct: 598 GQVRAVNCAAGDTVKEGETLIVTEAMKMEHSLTAPRDGIVAEVMAKAGDQVEEGAILLTL 657

Query: 657 MEEAA 661
            EE A
Sbjct: 658 EEEDA 662


Lambda     K      H
   0.319    0.135    0.394 

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: 1226
Number of extensions: 59
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: 662
Length of database: 662
Length adjustment: 38
Effective length of query: 624
Effective length of database: 624
Effective search space:   389376
Effective search space used:   389376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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