Aligments for a candidate for pccB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for pccB in Phaeobacter inhibens BS107

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF1015 PGA1_c10320 methylcrotonoyl-CoA carboxylase beta chain

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



>FitnessBrowser__Phaeo:GFF1015
          Length = 527

 Score =  701 bits (1810), Expect = 0.0
 Identities = 344/526 (65%), Positives = 402/526 (76%)

Query: 10  PNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSS 69
           P+S  F+ N   H      + E     R GGG + R RHE RGK+  R R+  L+DP S 
Sbjct: 2   PSSEGFKQNREAHLDALGQISEAAETARMGGGEKSRARHESRGKMLPRRRVANLLDPGSP 61

Query: 70  FLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQ 129
           FLEIGA AA+ +YD   P AG+V GIGRV G+ VM++ NDATVKGGTYFP+TVKKHLRAQ
Sbjct: 62  FLEIGATAAHAMYDGAAPGAGVVAGIGRVHGQEVMVVCNDATVKGGTYFPMTVKKHLRAQ 121

Query: 130 EIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCT 189
           EIA ENRLPCIYLVDSGGA LP Q EVFPDRDHFGRIFYNQA+MSA+GI QIA VMGSCT
Sbjct: 122 EIAEENRLPCIYLVDSGGANLPQQDEVFPDRDHFGRIFYNQARMSAKGIAQIAVVMGSCT 181

Query: 190 AGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFA 249
           AGGAYVPAMSD  +IVK  GTIFL GPPLVKAATGE V+AE+LGG DVHTR+SGVADY A
Sbjct: 182 AGGAYVPAMSDVTIIVKEQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSGVADYLA 241

Query: 250 NDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIAR 309
            DD  ALA+ R  V  L   +        PE P YDP EI G++P D R  YD+REVIAR
Sbjct: 242 EDDAHALALARRAVQSLNITKPLTVNWASPEEPAYDPEEILGVVPGDLRTPYDIREVIAR 301

Query: 310 IVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELCCARNIP 369
           +VDGSR  EFK R+G TLV GFAH++G PVGI+ANNG+LFSE+A KGAHF+ELC  R IP
Sbjct: 302 LVDGSRFDEFKPRFGETLVTGFAHVKGCPVGIIANNGVLFSEAAQKGAHFVELCSQRKIP 361

Query: 370 LVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMCGRAY 429
           LVFLQNITGFMVG++YEN GIA+ GAK+VTAV+  NVPK T+++GGSFGAGNYGM GRAY
Sbjct: 362 LVFLQNITGFMVGRKYENEGIARHGAKMVTAVATTNVPKVTMLVGGSFGAGNYGMSGRAY 421

Query: 430 QPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKYEQEG 489
           QPR LW WPN+RISVMGG QAA VL T++RD +  +G   + EE+  F  P +  +E++ 
Sbjct: 422 QPRFLWSWPNSRISVMGGEQAAGVLATVKRDAIERQGGSWSTEEEASFKQPTIDMFEEQS 481

Query: 490 HPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           HP YASARLWDDG+IDP ++R VLAL L+AA  AP++ TRFGVFRM
Sbjct: 482 HPLYASARLWDDGIIDPRKSRDVLALSLSAALNAPIEDTRFGVFRM 527


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: 946
Number of extensions: 37
Number of successful extensions: 2
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: 527
Length adjustment: 35
Effective length of query: 500
Effective length of database: 492
Effective search space:   246000
Effective search space used:   246000
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 Sep 17 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, or view the source code.

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