Alignments for a candidate for pccA in Brucella inopinata BO1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Brucella inopinata BO1

Align Propionyl-CoA carboxylase alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate WP_025199990.1 BIBO1_RS06830 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::P0DTA4
         (730 letters)



>NCBI__GCF_000182725.1:WP_025199990.1
          Length = 673

 Score =  487 bits (1253), Expect = e-142
 Identities = 301/674 (44%), Positives = 402/674 (59%), Gaps = 30/674 (4%)

Query: 63  FDKILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTMADEAVCVGPAPTSKSYL 122
           F KILIANRGEIACRVI+T +K+G+ TVA++SD DA ++HV MADEAV VGPA +++SYL
Sbjct: 20  FQKILIANRGEIACRVIRTARKLGVVTVAIYSDADARALHVEMADEAVRVGPAASAQSYL 79

Query: 123 NMDAIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDKIESKL 182
           N+DAI++A   T AQA+HPGYGFLSEN  F   +   G+IFIGP   AI+AMG K  +K 
Sbjct: 80  NVDAIIKAALETGAQAIHPGYGFLSENPAFVDAVEEAGLIFIGPSAKAIRAMGLKDAAKA 139

Query: 183 LAKKAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGF 242
           L +KA V  +PG+ G  +D       A  I YPV+IKA AGGGGKGMR      +     
Sbjct: 140 LMEKAGVPVVPGYHGDNQDGAFLKSEADRITYPVLIKARAGGGGKGMRRVDSAADFAAAL 199

Query: 243 RFSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEE 302
             + +EA +SFGD  +L+EK++  PRHIE+QV GD HGNA+ L ER+CS+QRR+QKV+EE
Sbjct: 200 ESARREAEASFGDGAVLVEKYMAKPRHIEVQVFGDNHGNAVHLFERDCSLQRRHQKVIEE 259

Query: 303 APSIFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKK-----NFYFLEMNTRLQVE 357
           AP+  +  E R AMGE AV  A A+ YS AGTVEF+ D  +      F+F+EMNTRLQVE
Sbjct: 260 APAPGMTEEMRAAMGEAAVKAALAIGYSGAGTVEFIADVSEGLRPDRFFFMEMNTRLQVE 319

Query: 358 HPVTECITGLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAEDPYKSFGLPSIGRL 417
           HPVTE ITGLDLV+  +RVA G  L  RQ ++ INGWA E R+YAEDP + F LP+ G+L
Sbjct: 320 HPVTEAITGLDLVEWQLRVASGEALPKRQDELSINGWAFEARLYAEDPARDF-LPATGKL 378

Query: 418 SQYQEPIHLPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALDNYVIRG 477
           + +  P      RVDSG++ G  I+ +YDPMI+K+IT+G+ R EAL R++ AL+   I G
Sbjct: 379 ALFVPP---ENARVDSGVRTGDTITPFYDPMIAKIITHGAMRDEALNRLDAALNKTRIAG 435

Query: 478 VTHNIALLREVIINSRFVEGDINTKFLSDVYPDGFKGHKLTEDERNQLLAIA-SSLFVAS 536
           +  N   L  +     F  GD++T  +      G +   L  D +   +A A ++L    
Sbjct: 436 LVTNRQFLSALCNLEAFRTGDVDTGLI------GRETAALFTDAQPSDIAFALAALGALD 489

Query: 537 QLRAQRFQEPENSRVPIIKPQVANWELSIRLHDEVHTVTASNSGPTFSVEVDGSKLNVTS 596
            L A    +P +          A+  + I  H +  TV+ +  G        G       
Sbjct: 490 LLDAPEKSDPWSGLRGFRLWGEASRSVLIEHHGKRRTVSFTARGDRHF----GFAFGTMD 545

Query: 597 TWNLASPLLSVSIDGTQRTIQCLSRDAGGNMSIQFLGTVYKVHILTKLAAELNKFMLEKA 656
                + L+  +IDG  R  +      G ++++Q  G     H +    A       E+ 
Sbjct: 546 IRKHKNGLVRFAIDG--RVSEASVLRIGHDVTVQIEGHDAIFHHVQATGA-------EED 596

Query: 657 AEDTSSILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAGKTGKVKSVHCKA 716
           A   S IL SPMPG+V  + V  G  VA+G  +  +EAMKM+ S+TA + GKV SV   A
Sbjct: 597 ASSESRIL-SPMPGLVRLICVVEGASVAKGDPLVTMEAMKMELSLTAPRDGKVASVTVAA 655

Query: 717 GDTVGEGDLLVELE 730
           GD V EG LLVELE
Sbjct: 656 GDQVNEGALLVELE 669


Lambda     K      H
   0.318    0.134    0.385 

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: 1079
Number of extensions: 46
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: 730
Length of database: 673
Length adjustment: 39
Effective length of query: 691
Effective length of database: 634
Effective search space:   438094
Effective search space used:   438094
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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Rules (tab-delimited)
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