Alignments for a candidate for acn in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Acidovorax sp. GW101-3H11

Align 2-methylisocitrate dehydratase (EC 4.2.1.99) (characterized)
to candidate Ac3H11_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Query= reanno::acidovorax_3H11:Ac3H11_1140
         (980 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1140
          Length = 980

 Score = 1951 bits (5055), Expect = 0.0
 Identities = 980/980 (100%), Positives = 980/980 (100%)

Query: 1   MATSRKSSPQPARHAFANTLKSFRTASGKDGQFYSLPALAKQFPEIKRLPVSIRIVLESV 60
           MATSRKSSPQPARHAFANTLKSFRTASGKDGQFYSLPALAKQFPEIKRLPVSIRIVLESV
Sbjct: 1   MATSRKSSPQPARHAFANTLKSFRTASGKDGQFYSLPALAKQFPEIKRLPVSIRIVLESV 60

Query: 61  LRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAK 120
           LRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAK
Sbjct: 61  LRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAK 120

Query: 121 LGKNPKKIEPLVPVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDT 180
           LGKNPKKIEPLVPVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDT
Sbjct: 121 LGKNPKKIEPLVPVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDT 180

Query: 181 FGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIE 240
           FGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIE
Sbjct: 181 FGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIE 240

Query: 241 AEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGT 300
           AEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGT
Sbjct: 241 AEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGT 300

Query: 301 RTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGV 360
           RTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGV
Sbjct: 301 RTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGV 360

Query: 361 PLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAE 420
           PLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAE
Sbjct: 361 PLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAE 420

Query: 421 LLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGA 480
           LLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGA
Sbjct: 421 LLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGA 480

Query: 481 DPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTE 540
           DPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTE
Sbjct: 481 DPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTE 540

Query: 541 YLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEA 600
           YLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEA
Sbjct: 541 YLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEA 600

Query: 601 RIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALL 660
           RIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALL
Sbjct: 601 RIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALL 660

Query: 661 KFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANK 720
           KFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANK
Sbjct: 661 KFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANK 720

Query: 721 ASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKAD 780
           ASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKAD
Sbjct: 721 ASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKAD 780

Query: 781 FNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFD 840
           FNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFD
Sbjct: 781 FNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFD 840

Query: 841 AAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVL 900
           AAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVL
Sbjct: 841 AAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVL 900

Query: 901 PLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGTVREVVVTLRIDTPIE 960
           PLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGTVREVVVTLRIDTPIE
Sbjct: 901 PLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGTVREVVVTLRIDTPIE 960

Query: 961 VDYYRAGGILPFVLRQLLEG 980
           VDYYRAGGILPFVLRQLLEG
Sbjct: 961 VDYYRAGGILPFVLRQLLEG 980


Lambda     K      H
   0.318    0.136    0.399 

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: 3089
Number of extensions: 89
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: 980
Length of database: 980
Length adjustment: 44
Effective length of query: 936
Effective length of database: 936
Effective search space:   876096
Effective search space used:   876096
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: 57 (26.6 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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