Alignments for a candidate for pccA in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Brucella microti CCM 4915

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012783807.1 BMI_RS00080 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000022745.1:WP_012783807.1
          Length = 673

 Score =  504 bits (1299), Expect = e-147
 Identities = 301/678 (44%), Positives = 396/678 (58%), Gaps = 39/678 (5%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MF+KILIANRGEIACRVI+TARK+GI TVA+YSDAD  ALHV MADEA+ +GP  + QSY
Sbjct: 19  MFQKILIANRGEIACRVIRTARKLGIATVAIYSDADARALHVEMADEAVRVGPAASAQSY 78

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           + +D I++A K +GAEA+HPGYGFLSE   F  A+E AG++FIGP + AI AMG K  +K
Sbjct: 79  LNVDAIIKAAKETGAEAIHPGYGFLSENPAFVDAVEEAGLIFIGPSAKAIRAMGLKDAAK 138

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
            L ++AGV  VPGY G   D       ++ I YPV+IKA AGGGGKGMR   S A+    
Sbjct: 139 ALMEKAGVPVVPGYHGDNQDGAFLKSEADRITYPVLIKARAGGGGKGMRRVDSAADFAAA 198

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
            ES++ EA  SFGD  + +EK++ +PRHIE+QV  D HGN V+L ER+CS+QRR+QKVIE
Sbjct: 199 LESARREAEASFGDGAVLVEKYMAKPRHIEVQVFGDNHGNAVHLFERDCSLQRRHQKVIE 258

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQK-----NFYFLEMNTRLQV 295
           EAP+P + E  R AMGE A   A  +GY+ AGTVEFI D  +      F+F+EMNTRLQV
Sbjct: 259 EAPAPGMTEEMRAAMGEAAVKAALTIGYSGAGTVEFIADVSEGLRPDRFFFMEMNTRLQV 318

Query: 296 EHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRL 355
           EHPVTE ITG+DLVE  +RVA+GE LP +Q +L INGWA E+RLYAEDP R+FLP+ G+L
Sbjct: 319 EHPVTEAITGLDLVEWQLRVASGEALPKRQDELSINGWAFEARLYAEDPARDFLPATGKL 378

Query: 356 TRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTF 415
             + PP  +       R D+GV  G  I+ +YDPMIAK+ T   TR+ A+  +  AL+  
Sbjct: 379 ALFVPPENA-------RVDSGVRTGDTITPFYDPMIAKIITHGATRDEALNRLDAALNKT 431

Query: 416 EVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMN 475
            + G+  N  F+ A+ +   F  GD+ T  I          A+  +     +A A AA+ 
Sbjct: 432 RIAGLVTNRQFLSALCNLEAFRTGDVDTGLIGRGL-----AALFTDAQPSDIAFALAALG 486

Query: 476 RVAEIRRTRISGTMNNHERHVGVDWVVALQGE-SYHVSIAADREGSTVSFSD------GS 528
            +  +     S   +             L GE S  V I    E  TVSF+       G 
Sbjct: 487 ALDLLDAPEKSDPWSGLRG-------FRLWGEASRSVLIEHHGERRTVSFTARGDRHFGF 539

Query: 529 SLRVTSDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLM 588
           +          + L    +DGR     V +I     +++ G D   +      AE     
Sbjct: 540 AFGTMDIRAHKKGLVRFAIDGRVSEASVSRIGHDVTVQIEGHDTIFHHVLATGAE----- 594

Query: 589 PEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKI 648
                  +   +L PMPGLV  ++V EG  V +G  L T+EAMKME  L A R G V  +
Sbjct: 595 ---EDASSESRILSPMPGLVRLVSVVEGASVAKGDPLVTMEAMKMELSLTAPRDGKVASV 651

Query: 649 AAAPGASLRVDDVIMEFE 666
             A G  +    +++E E
Sbjct: 652 TVAAGDQVNEGALLVELE 669


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: 1067
Number of extensions: 46
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 666
Length of database: 673
Length adjustment: 39
Effective length of query: 627
Effective length of database: 634
Effective search space:   397518
Effective search space used:   397518
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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