Alignments for a candidate for ech in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Marinobacter adhaerens HP15

Align Enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF1550 HP15_1512 multifunctional fatty acid oxidation complex subunit alpha

Query= reanno::Marino:GFF1550
         (715 letters)



>FitnessBrowser__Marino:GFF1550
          Length = 715

 Score = 1415 bits (3663), Expect = 0.0
 Identities = 715/715 (100%), Positives = 715/715 (100%)

Query: 1   MIYEGKAITVKEIEGGIAQLNFDLQGESVNKFNRLTIEELRAATDALKAQKNLKGLVVTS 60
           MIYEGKAITVKEIEGGIAQLNFDLQGESVNKFNRLTIEELRAATDALKAQKNLKGLVVTS
Sbjct: 1   MIYEGKAITVKEIEGGIAQLNFDLQGESVNKFNRLTIEELRAATDALKAQKNLKGLVVTS 60

Query: 61  SKDSFIVGADITEFTELFAGSEEDLVANNLKANEVFNAVEDLPFPTVTAINGMALGGGFE 120
           SKDSFIVGADITEFTELFAGSEEDLVANNLKANEVFNAVEDLPFPTVTAINGMALGGGFE
Sbjct: 61  SKDSFIVGADITEFTELFAGSEEDLVANNLKANEVFNAVEDLPFPTVTAINGMALGGGFE 120

Query: 121 MCLATDYRVMDKKAKVGLPEVKLGIFPGFGGTVRLSRLVGVDNAVEWISGGTENRADVAL 180
           MCLATDYRVMDKKAKVGLPEVKLGIFPGFGGTVRLSRLVGVDNAVEWISGGTENRADVAL
Sbjct: 121 MCLATDYRVMDKKAKVGLPEVKLGIFPGFGGTVRLSRLVGVDNAVEWISGGTENRADVAL 180

Query: 181 KVGAVDAVLDSDKLVDAAVAIINQCNEGKLDHEARREEKKGKIKLNAMESMMAFEISKAF 240
           KVGAVDAVLDSDKLVDAAVAIINQCNEGKLDHEARREEKKGKIKLNAMESMMAFEISKAF
Sbjct: 181 KVGAVDAVLDSDKLVDAAVAIINQCNEGKLDHEARREEKKGKIKLNAMESMMAFEISKAF 240

Query: 241 VAGKAGKNYPAPVEAIKVMQKHAGMTRDKAIEVEAKGFAKMAKTNVAACLVGLFLNDQEL 300
           VAGKAGKNYPAPVEAIKVMQKHAGMTRDKAIEVEAKGFAKMAKTNVAACLVGLFLNDQEL
Sbjct: 241 VAGKAGKNYPAPVEAIKVMQKHAGMTRDKAIEVEAKGFAKMAKTNVAACLVGLFLNDQEL 300

Query: 301 KKKAKAWEKEANDVNLAAVLGAGIMGGGVAFQSALKGTPIIMKDINQDGIALGLKEAKKL 360
           KKKAKAWEKEANDVNLAAVLGAGIMGGGVAFQSALKGTPIIMKDINQDGIALGLKEAKKL
Sbjct: 301 KKKAKAWEKEANDVNLAAVLGAGIMGGGVAFQSALKGTPIIMKDINQDGIALGLKEAKKL 360

Query: 361 LSKRVEKGKMKPDQMADVLNSITPTLNYGDFKNVDLVVEAVVENPKVKDAVLRETEDAVR 420
           LSKRVEKGKMKPDQMADVLNSITPTLNYGDFKNVDLVVEAVVENPKVKDAVLRETEDAVR
Sbjct: 361 LSKRVEKGKMKPDQMADVLNSITPTLNYGDFKNVDLVVEAVVENPKVKDAVLRETEDAVR 420

Query: 421 EDTILTSNTSTISIDLLAKNLKRPENFCGMHFFNPVHMMPLVEVIRGEKTSDRAIATTVA 480
           EDTILTSNTSTISIDLLAKNLKRPENFCGMHFFNPVHMMPLVEVIRGEKTSDRAIATTVA
Sbjct: 421 EDTILTSNTSTISIDLLAKNLKRPENFCGMHFFNPVHMMPLVEVIRGEKTSDRAIATTVA 480

Query: 481 YAKAMGKTPIVVNDCPGFLVNRVLFPYFGGFIGLVRDGADFQHVDKVMEKFGWPMGPAYL 540
           YAKAMGKTPIVVNDCPGFLVNRVLFPYFGGFIGLVRDGADFQHVDKVMEKFGWPMGPAYL
Sbjct: 481 YAKAMGKTPIVVNDCPGFLVNRVLFPYFGGFIGLVRDGADFQHVDKVMEKFGWPMGPAYL 540

Query: 541 LDVVGMDTGKHAGEVMADGFPDRMKHEGTTAIDVMFDNNRYGQKNDKGFYKYELDRKGKQ 600
           LDVVGMDTGKHAGEVMADGFPDRMKHEGTTAIDVMFDNNRYGQKNDKGFYKYELDRKGKQ
Sbjct: 541 LDVVGMDTGKHAGEVMADGFPDRMKHEGTTAIDVMFDNNRYGQKNDKGFYKYELDRKGKQ 600

Query: 601 KKVVDEETYKLLEPVVQGKNEFSEEDIIARMMIPLCLETVRCLEDGIVEDPADADMGLIF 660
           KKVVDEETYKLLEPVVQGKNEFSEEDIIARMMIPLCLETVRCLEDGIVEDPADADMGLIF
Sbjct: 601 KKVVDEETYKLLEPVVQGKNEFSEEDIIARMMIPLCLETVRCLEDGIVEDPADADMGLIF 660

Query: 661 GIGFPPFRGGALRYIDDMGVDKFVELADKFADLGPLYHPTEKLREMAKTGKKFFG 715
           GIGFPPFRGGALRYIDDMGVDKFVELADKFADLGPLYHPTEKLREMAKTGKKFFG
Sbjct: 661 GIGFPPFRGGALRYIDDMGVDKFVELADKFADLGPLYHPTEKLREMAKTGKKFFG 715


Lambda     K      H
   0.318    0.137    0.391 

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: 1821
Number of extensions: 73
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: 715
Length of database: 715
Length adjustment: 39
Effective length of query: 676
Effective length of database: 676
Effective search space:   456976
Effective search space used:   456976
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: 55 (25.8 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