Alignments for a candidate for ydiJ in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Pseudomonas putida KT2440

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate PP_4493 PP_4493 putative oxidoreductase

Query= reanno::Putida:PP_4493
         (1006 letters)



>FitnessBrowser__Putida:PP_4493
          Length = 1006

 Score = 2032 bits (5265), Expect = 0.0
 Identities = 1006/1006 (100%), Positives = 1006/1006 (100%)

Query: 1    MIAQLSTVAPSANYPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDA 60
            MIAQLSTVAPSANYPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDA
Sbjct: 1    MIAQLSTVAPSANYPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDA 60

Query: 61   DDVARVATLMGEPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVR 120
            DDVARVATLMGEPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVR
Sbjct: 61   DDVARVATLMGEPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVR 120

Query: 121  VQAGTVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELH 180
            VQAGTVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELH
Sbjct: 121  VQAGTVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELH 180

Query: 181  SVLLGGERLHSLPIDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTG 240
            SVLLGGERLHSLPIDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTG
Sbjct: 181  SVLLGGERLHSLPIDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTG 240

Query: 241  YDLAHLRDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDA 300
            YDLAHLRDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDA
Sbjct: 241  YDLAHLRDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDA 300

Query: 301  NALMAHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVN 360
            NALMAHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVN
Sbjct: 301  NALMAHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVN 360

Query: 361  AKVQAFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDT 420
            AKVQAFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDT
Sbjct: 361  AKVQAFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDT 420

Query: 421  AVPPEQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAV 480
            AVPPEQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAV
Sbjct: 421  AVPPEQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAV 480

Query: 481  AALTKRYGGLLWGEHGKGLRSEYVPEYFGELYPALQRLKGAFDPHNQLNPGKICTPLGSA 540
            AALTKRYGGLLWGEHGKGLRSEYVPEYFGELYPALQRLKGAFDPHNQLNPGKICTPLGSA
Sbjct: 481  AALTKRYGGLLWGEHGKGLRSEYVPEYFGELYPALQRLKGAFDPHNQLNPGKICTPLGSA 540

Query: 541  EGLTPVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQH 600
            EGLTPVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQH
Sbjct: 541  EGLTPVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQH 600

Query: 601  SPKGRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYD 660
            SPKGRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYD
Sbjct: 601  SPKGRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYD 660

Query: 661  AMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPG 720
            AMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPG
Sbjct: 661  AMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPG 720

Query: 721  LYNAVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERS 780
            LYNAVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERS
Sbjct: 721  LYNAVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERS 780

Query: 781  IVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNA 840
            IVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNA
Sbjct: 781  IVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNA 840

Query: 841  TQLKALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKVLLPQEWLMDVLPEQAPAAPG 900
            TQLKALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKVLLPQEWLMDVLPEQAPAAPG
Sbjct: 841  TQLKALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKVLLPQEWLMDVLPEQAPAAPG 900

Query: 901  SFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIF 960
            SFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIF
Sbjct: 901  SFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIF 960

Query: 961  EQSWATKLDKDGEPLATGYSCRSQVKRMTERKMRHPLEVVLQYAQR 1006
            EQSWATKLDKDGEPLATGYSCRSQVKRMTERKMRHPLEVVLQYAQR
Sbjct: 961  EQSWATKLDKDGEPLATGYSCRSQVKRMTERKMRHPLEVVLQYAQR 1006


Lambda     K      H
   0.320    0.135    0.409 

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: 3181
Number of extensions: 83
Number of successful extensions: 1
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: 1006
Length of database: 1006
Length adjustment: 45
Effective length of query: 961
Effective length of database: 961
Effective search space:   923521
Effective search space used:   923521
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 (21.8 bits)
S2: 57 (26.6 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