Alignments for a candidate for pccA in Oleispira antarctica

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Oleispira antarctica

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_046008864.1 OLEAN_RS08430 carbamoyl phosphate synthase large subunit

Query= reanno::PS:Dsui_0516
         (663 letters)



>NCBI__GCF_000967895.1:WP_046008864.1
          Length = 1649

 Score =  297 bits (760), Expect = 3e-84
 Identities = 171/450 (38%), Positives = 259/450 (57%), Gaps = 12/450 (2%)

Query: 3    KKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMA---DEAVCIGPAASKES 59
            KK++I  RG  A ++IK A+   I  V V S+ D +++ V+M    D  VCIG     ES
Sbjct: 1068 KKVMIHARGCTAAKLIKKAQDNNIPVVLVQSDPDMNSVAVDMLGPEDRVVCIGGNTPDES 1127

Query: 60   YLVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIES 119
            YL A  +I   +    +A+HPG GFLSE+++F+      GI F+GP   S+  MG+K  +
Sbjct: 1128 YLNAKSVIRIAQHEQVDALHPGIGFLSESSQFAALCASYGINFVGPSVSSMETMGNKSNA 1187

Query: 120  KKLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHE 179
               AI A V  +PG +  +        +A+ IGYPV++KA  GGGGKG++V     + HE
Sbjct: 1188 INTAIAANVPVVPGSHGILTSSANTASVAEDIGYPVLLKAVHGGGGKGIQVVERPEQIHE 1247

Query: 180  GFSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVI 239
             F     EA+ +FG+  V++EKYV   RHIE+QVL D  G+   L  RDCS+QR +QKV 
Sbjct: 1248 LFHQISTEAKAAFGNGDVYLEKYVTSLRHIEVQVLRDRFGHTKILGLRDCSVQRNNQKVF 1307

Query: 240  EEAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHP 299
            EE+ S  +   + +A+ + A  L+ AV+Y  AGTVEF+ +      YF+EMNTRLQVEHP
Sbjct: 1308 EESGSTMLPKALEQAVYDYAEKLSDAVDYFGAGTVEFIYNLDEDAIYFMEMNTRLQVEHP 1367

Query: 300  VTELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFR-----GFLPSTG 354
            VTE+++G+D+V     +A G+   + +   +  G+A+E R+ AE   R      F P  G
Sbjct: 1368 VTEVVSGIDIVSAQFDIAQGKS--IAKLKPKPKGYAIEVRVTAEKAVRKGDLIDFAPFPG 1425

Query: 355  RLVKFQPPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFV 414
             + +   P E+D  +++ T    G ++S +YDSMI ++I +G  R+  IA++R  L+   
Sbjct: 1426 TINECVLP-ELD-HIQLITSAGPGKQVSPFYDSMIVQIICYGKDRDDTIAKLRTYLDQVR 1483

Query: 415  IRGISSNIPFQAALMQHARFQSGIFDTGFI 444
            I G+ +NI     ++    FQ G +DT ++
Sbjct: 1484 ITGVCTNIVLLKRILDDKIFQLGDYDTTYL 1513


Lambda     K      H
   0.319    0.135    0.391 

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: 2168
Number of extensions: 100
Number of successful extensions: 3
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: 663
Length of database: 1649
Length adjustment: 45
Effective length of query: 618
Effective length of database: 1604
Effective search space:   991272
Effective search space used:   991272
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 (21.7 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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 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