Alignments for a candidate for pccB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Dinoroseobacter shibae DFL-12

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate 3607892 Dshi_1300 Propionyl-CoA carboxylase (RefSeq)

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



>FitnessBrowser__Dino:3607892
          Length = 534

 Score =  668 bits (1723), Expect = 0.0
 Identities = 327/519 (63%), Positives = 389/519 (74%)

Query: 17  ANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSSFLEIGAL 76
           AN A H +  A + +  A    GGG   R RH  RGK+  RDR+  L+DP S FLE+GA 
Sbjct: 16  ANRAAHLAALAQVSQVAALAAAGGGEAARARHVARGKMLPRDRVANLLDPGSPFLEVGAT 75

Query: 77  AAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQEIARENR 136
           A + ++D   P  G + G+GRV G+ VM++ NDATVKGGTY+P+TVKKHLRAQEIA E  
Sbjct: 76  AGHGLHDGAAPCGGAIAGVGRVHGQDVMVVCNDATVKGGTYYPITVKKHLRAQEIAAECH 135

Query: 137 LPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCTAGGAYVP 196
           LPCIYLVDSGGA LP Q EVFPDRDHFGRIFYNQA+MSA GIPQIA VMGSCTAGGAYVP
Sbjct: 136 LPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQARMSAAGIPQIAVVMGSCTAGGAYVP 195

Query: 197 AMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFANDDREAL 256
           AMSD  +IVK  GTIFL GPPLVKAATGE V+AE+LGG DVHTR+SGVAD  A DD  AL
Sbjct: 196 AMSDVTIIVKAQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSGVADALAEDDAHAL 255

Query: 257 AIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIARIVDGSRL 316
           A+ R  VA L     ++   + PE P YDP E+  ++P      YD+ EVIARIVDGSR 
Sbjct: 256 ALARQAVASLNRAAPSSVVWQSPEAPAYDPEELLELVPASLSVPYDIHEVIARIVDGSRF 315

Query: 317 HEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELCCARNIPLVFLQNI 376
             FK R+G TLV GFAHIEG PVGI+ANNG+LFSE+A KGAHF+ELC  R IPLVFLQNI
Sbjct: 316 DAFKPRFGETLVTGFAHIEGCPVGIVANNGVLFSEAAQKGAHFVELCSQRKIPLVFLQNI 375

Query: 377 TGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMCGRAYQPRQLWM 436
           TGFMVG+QYEN GIA+ GAK+VTAV+   VPK T+++GGSFGAGNYGM GRAYQPR +W 
Sbjct: 376 TGFMVGRQYENEGIARHGAKMVTAVATTAVPKITMVVGGSFGAGNYGMAGRAYQPRFMWS 435

Query: 437 WPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKYEQEGHPYYASA 496
           WP++RISVMGG QAA VL T++RD +  +G   + +E+  F  P +  +E + HP YASA
Sbjct: 436 WPSSRISVMGGAQAAGVLATVKRDAIERKGGSWSAQEEAAFKQPTIEMFEAQSHPLYASA 495

Query: 497 RLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           RLWDDG++DP ++R VL+L L AA  AP++ TRFGVFRM
Sbjct: 496 RLWDDGIVDPRKSRAVLSLSLRAALNAPIEETRFGVFRM 534


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: 951
Number of extensions: 36
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: 535
Length of database: 534
Length adjustment: 35
Effective length of query: 500
Effective length of database: 499
Effective search space:   249500
Effective search space used:   249500
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
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