GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Caulobacter crescentus NA1000

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate CCNA_01875 CCNA_01875 acyl-CoA dehydrogenase, short-chain specific

Query= reanno::Phaeo:GFF1011
         (386 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01875 CCNA_01875 acyl-CoA
           dehydrogenase, short-chain specific
          Length = 381

 Score =  270 bits (691), Expect = 4e-77
 Identities = 142/375 (37%), Positives = 226/375 (60%), Gaps = 1/375 (0%)

Query: 12  EDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFGGAGMSY 71
           + ++AL D++ R+  ER+RP+   + + +E P  + +EM +LGL G+++PE +GG G+S 
Sbjct: 5   DTLSALIDVIQRFVAERLRPIEGLVSETDEVPGSIIEEMKQLGLFGLSIPESYGGLGLSL 64

Query: 72  LAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLVSGEHVGALAMS 131
                 +      + +   ++G +  +    + + G+  QKA++LP + SGE + A A++
Sbjct: 65  EEEARVIVAFCHTAPAFRSTFGTNVGIGSQGLVMFGDEAQKARWLPSIASGETITAFALT 124

Query: 132 EAGAGSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDA-GSKGMTAFL 190
           EA AGSD  S+  RA +  DHY LNG K +ITN   A+   V A+TDP+  G  G++AFL
Sbjct: 125 EAEAGSDSASVQTRAVRDGDHYVLNGVKRYITNAGRANLFTVMARTDPNTKGGAGVSAFL 184

Query: 191 IEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLDYERVV 250
           +  +  G S  +   K+G +G++  ++VFEDV VP EN LG EG+G  V M  LD  RV 
Sbjct: 185 VPADLPGLSVGKPEKKMGQQGAHIHDVVFEDVRVPVENRLGAEGEGFTVAMRVLDRGRVH 244

Query: 251 LAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVYEVAKA 310
           ++ +  G+    + + + Y  ERKQFGQPI +FQL+Q  IAD  T    A+A V++ A+ 
Sbjct: 245 ISAVCVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIADSKTEALAAKALVFDTARK 304

Query: 311 CDKGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLMEIGAGT 370
            D G     +AAA  L+ASE+    A +AVQ FGGAGY++D  + R++RD ++  I  G 
Sbjct: 305 RDAGANVTLEAAATKLFASEMVGRVADRAVQVFGGAGYVADYGIERLYRDVRIFRIYEGA 364

Query: 371 SEIRRMLIGRELMSQ 385
           S+I++++I RE + +
Sbjct: 365 SQIQQLIIARETLKR 379


Lambda     K      H
   0.318    0.132    0.382 

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: 352
Number of extensions: 17
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: 386
Length of database: 381
Length adjustment: 30
Effective length of query: 356
Effective length of database: 351
Effective search space:   124956
Effective search space used:   124956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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