Alignments for a candidate for pccB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Sphingomonas koreensis DSMZ 15582

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Ga0059261_4055 Ga0059261_4055 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)

Query= metacyc::MONOMER-17283
         (535 letters)



>FitnessBrowser__Korea:Ga0059261_4055
          Length = 533

 Score =  712 bits (1839), Expect = 0.0
 Identities = 353/534 (66%), Positives = 417/534 (78%), Gaps = 6/534 (1%)

Query: 3   IIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDT 62
           ++ S + P    F+ N A++++LA  L   +AQ   GG  + R RH  RGKL  R+R++ 
Sbjct: 5   VLRSALSPEDEGFRTNAAHNRALAEKLHADVAQAALGGNEKSRERHTSRGKLLPRERVER 64

Query: 63  LIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTV 122
           L+DP S FLEIG LAA ++Y+ EVP AG++ GIGRV+GR  MI+ NDATVKGGTY+P+TV
Sbjct: 65  LLDPGSPFLEIGQLAACDMYEGEVPGAGMIAGIGRVSGRQCMIVCNDATVKGGTYYPMTV 124

Query: 123 KKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIA 182
           KKHLRAQEIA  NRLPCIYLVDSGGA LP Q+EVFPD++HFGRIF+NQA MSA+GIPQIA
Sbjct: 125 KKHLRAQEIAEANRLPCIYLVDSGGANLPHQAEVFPDKEHFGRIFFNQANMSAKGIPQIA 184

Query: 183 CVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRIS 242
           CVMGSCTAGGAYVPAMSDE VIV+  GTIFL GPPLVKAATGEE++AE+LGG D+H R S
Sbjct: 185 CVMGSCTAGGAYVPAMSDESVIVRNQGTIFLAGPPLVKAATGEEISAEDLGGGDLHGRKS 244

Query: 243 GVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYD 302
           GV D+ A +D  AL IVRDIV+HL   +  +  + DP PP++D  E+YGI+P D R  YD
Sbjct: 245 GVVDHVAENDEHALTIVRDIVSHLPRDRTPDVAILDPRPPKFDAEELYGIVPTDVRAPYD 304

Query: 303 VREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIEL 362
           V EVIARIVDGS  HEFK  YG+TLVCGFAHI G PV ILANNG+LFSESA+KGAHFIEL
Sbjct: 305 VHEVIARIVDGSEFHEFKAPYGSTLVCGFAHIWGMPVAILANNGVLFSESAVKGAHFIEL 364

Query: 363 CCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNY 422
            C R IPL+FLQNI+GFMVG +YE  GIAK GAKLVTAV+ A+VPK TV+IGGSFGAGNY
Sbjct: 365 ACQRRIPLLFLQNISGFMVGGKYEAEGIAKHGAKLVTAVATASVPKITVLIGGSFGAGNY 424

Query: 423 GMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPIL 482
           GMCGRAY PR L+ WPN+RISVMGG QAA+VL T+ RD         TPE+ E F API 
Sbjct: 425 GMCGRAYSPRFLFSWPNSRISVMGGEQAASVLATVHRD-----ADSWTPEQAETFKAPIR 479

Query: 483 AKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQP-TRFGVFRM 535
            KYE EG+P++A+ARLWDDG+IDP +TR VL L  AA   APV+  TRFGVFRM
Sbjct: 480 QKYEDEGNPWHATARLWDDGIIDPAQTRDVLGLAFAATLNAPVEEGTRFGVFRM 533


Lambda     K      H
   0.322    0.139    0.423 

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: 962
Number of extensions: 40
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: 535
Length of database: 533
Length adjustment: 35
Effective length of query: 500
Effective length of database: 498
Effective search space:   249000
Effective search space used:   249000
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 (21.9 bits)
S2: 52 (24.6 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