Alignments for a candidate for pccA in Halioglobus japonicus S1-36

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Halioglobus japonicus S1-36

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_084200258.1 C0029_RS03860 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_002869505.1:WP_084200258.1
          Length = 658

 Score =  496 bits (1278), Expect = e-144
 Identities = 297/665 (44%), Positives = 391/665 (58%), Gaps = 23/665 (3%)

Query: 4   KILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYLVA 63
           K+LIANRGEIA RVI+TAR MG +TVAVYSEAD +AL V  AD+AVCIGPAA  ESYLVA
Sbjct: 6   KLLIANRGEIAVRVIRTARDMGYRTVAVYSEADANALHVSEADQAVCIGPAAVNESYLVA 65

Query: 64  DKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKKLA 123
           D I+ A + TGA+A+HPGYGFLSENA+FSR  E+ GI FIGP+  +I  MG K  SK   
Sbjct: 66  DNILKAARLTGADAIHPGYGFLSENADFSRACEDAGIVFIGPRPDAIELMGSKRLSKIAM 125

Query: 124 IEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGFSS 183
           IEA V  IPGY DA    D  +  A  IG+P+M+KASAGGGG+G+R+ +   E  E   +
Sbjct: 126 IEAGVPCIPGYQDADQSDDTLLAKAADIGFPLMVKASAGGGGRGMRLVFEARELAEQIRT 185

Query: 184 CVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEEAP 243
             +EA ++FG   + +E+ VLEPRH+EIQV  D HGN VYL ERDCSIQRRHQKV+EEAP
Sbjct: 186 ARSEAESAFGSGELILERAVLEPRHVEIQVFADEHGNAVYLGERDCSIQRRHQKVVEEAP 245

Query: 244 SPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVTEL 303
           SPFVDP++R+ MGE AV  A+A NY  AGTVEF+V    K FYFLEMNTRLQVEHPVTEL
Sbjct: 246 SPFVDPQLRQRMGEAAVNAAKACNYRGAGTVEFLVD-KDKNFYFLEMNTRLQVEHPVTEL 304

Query: 304 ITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQPPA 363
           ITG DLV   ++VA GE+LPLTQ +V ++G A+E R+ AEDP   F+P TG +  ++ P 
Sbjct: 305 ITGQDLVAWQLKVASGEQLPLTQDEVSLSGHAVEVRLYAEDPRNNFMPQTGTVRLWEYPE 364

Query: 364 EVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSNIP 423
                +R+D G+  G E+S +YD MIAK+I +G+ R +AI R+  A+    + G+++N  
Sbjct: 365 RAG--LRMDHGIQQGQEVSPFYDPMIAKVIAYGSDRAEAIRRLASAVQDTQLLGMNNNKL 422

Query: 424 FQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRAAQV 483
           F   +++H  F  G   T FI + +    D SM         +  AA + +     A   
Sbjct: 423 FLQNVLRHEVFAQGEATTAFIEQHF--SADISMDQKKPRQATLARAALLFQAQATAAGPG 480

Query: 484 SGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYEL----LSDWRQGQSL 539
           S     +       + +  +G+   +      G Y V    E++ L    LSD  +   +
Sbjct: 481 SDASWHNPAAAATTYQLAFDGQAQAIAITEGNGSYEVAVGEERHSLTLVALSD-SECVYI 539

Query: 540 FNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDL-SKFLL 598
            NG      F        +     H+              E +   P  AA    S  L 
Sbjct: 540 DNGVRESMRFAFAGNTLYLDDGTGHF------------IIENVTYQPAAAAGGAGSGQLK 587

Query: 599 SPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEI 658
           + M G + +V V  G  V+AG+ L V+EAMKME+ LKA     V  IS   G  +   ++
Sbjct: 588 ASMDGAIVDVLVTEGDTVEAGQTLVVLEAMKMEHALKAGISGIVTAISCETGQQVKSKQL 647

Query: 659 IIEFE 663
           +   E
Sbjct: 648 LATIE 652


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: 1053
Number of extensions: 53
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: 663
Length of database: 658
Length adjustment: 38
Effective length of query: 625
Effective length of database: 620
Effective search space:   387500
Effective search space used:   387500
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: 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)
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