Alignments for a candidate for pccA in Phaeacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Phaeacidiphilus oryzae TH49

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_037571256.1 BS73_RS10225 carboxyl transferase domain-containing protein

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_000744815.1:WP_037571256.1
          Length = 1084

 Score =  364 bits (935), Expect = e-105
 Identities = 232/601 (38%), Positives = 321/601 (53%), Gaps = 68/601 (11%)

Query: 5   VLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDHE 64
           VLVANRGEIAVR++RA  E G+R+VA Y+E +    H R ADEA  + P     +YLD  
Sbjct: 6   VLVANRGEIAVRIVRAAAEAGLRSVAGYAEDEPEAAHARLADEAVPL-PGSGPAAYLDGP 64

Query: 65  SVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLMQ 124
            +   A +A  + +HPGYGFL+E+A FAR   +    +VGP+ + +E LG+K +AR+L +
Sbjct: 65  GIAAVAAEAGCELLHPGYGFLSEDAGFARACAERGVGFVGPAPEVLELLGDKARARALAK 124

Query: 125 DADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFETA 184
              VPV+PGT EP +     + +  ++G  + +KA GGGGGRGL+ V   + +   ++  
Sbjct: 125 SLGVPVLPGT-EPGEGIGAARRLLAEHG-SLMVKAVGGGGGRGLRAVRDPEGLAEAWQRC 182

Query: 185 KREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEAPS 244
             E    F  A VY E+ L   RHIEVQ+L D  G V HL ERDCS QRR+QK+IE AP+
Sbjct: 183 ASEAGTAFGRAEVYAERLLTGARHIEVQVLGDGTGAVSHLWERDCSAQRRNQKLIELAPA 242

Query: 245 PALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTEEVTG 304
           P L   LR+R+  AA R      Y   GT EFLV+DG F+F+E N R+QVEHTVTEEVTG
Sbjct: 243 PGLDPALRDRLIGAALRLAGEVAYRGLGTFEFLVQDGGFWFLEANPRLQVEHTVTEEVTG 302

Query: 305 LDVVKWQLRVAAGEELD---FSQDDVEIEGHSMEFRINAE--APEKEFAPATGTLSTYDP 359
           +D+V  QLR+A GE LD    +       G +++ R+ AE   P+ E  P+ GTL  +D 
Sbjct: 303 VDLVAAQLRIAVGETLDALGLAGPPPAPRGSAVQLRLYAERLGPDGEARPSAGTLRRFDL 362

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           P G G+R+D A R GD +G  YD ++AK++V G      + RA RAL E  ++G+RT   
Sbjct: 363 PTGPGVRVDTACRPGDAVGVRYDPLLAKIVVRGGSPSAAVERARRALAELRVDGVRTGAA 422

Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEVTERTFTVEV 479
               +L                                PE  AG    G V E      V
Sbjct: 423 LLEAVLA------------------------------LPELPAGRVHTGRVAELVAAGGV 452

Query: 480 NGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQQVIEGDGESVAAEM 539
            G   +   EE      PLG                  E+  EG       D  +V A +
Sbjct: 453 AGAAGDEPPEE------PLG------------------EDEGEG------EDTAAVRAPL 482

Query: 540 QGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVLLV 599
            GT+L+++V   + V  G  + +LEAMKME+ V A   G+V ++    G++VD G +L +
Sbjct: 483 AGTVLSLDVAVAEQVGRGQRLMVLEAMKMEHVVRAPAAGSVLRLPAAVGETVDEGVLLAL 542

Query: 600 L 600
           L
Sbjct: 543 L 543


Lambda     K      H
   0.312    0.132    0.371 

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: 1552
Number of extensions: 93
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: 601
Length of database: 1084
Length adjustment: 41
Effective length of query: 560
Effective length of database: 1043
Effective search space:   584080
Effective search space used:   584080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. 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 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