Alignments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Dyella japonica UNC79MFTsu3.2

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate N515DRAFT_0029 N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0029
          Length = 869

 Score = 1511 bits (3912), Expect = 0.0
 Identities = 756/873 (86%), Positives = 808/873 (92%), Gaps = 11/873 (1%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  R+ L GT LDYFDARAAVEAIQPGAYD LPYTSRVLAENLVRRCDPA L +SL Q
Sbjct: 1   MNTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RKR+ DFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPAKVNPVVPVQLIVDH
Sbjct: 61  IIERKRERDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDP+AFA+NRAIEDRRNEDRFHFI+WT+QAF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPNAFARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADN-----GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 235
           SPVI   +     GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP
Sbjct: 181 SPVIQVQHDDQGKGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 240

Query: 236 DIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMA 295
           DI+GVELTGKRQPGITATDIVLALTEFLR+EKVVGAYLEFRGEGA+SLTLGDRATISNMA
Sbjct: 241 DIIGVELTGKRQPGITATDIVLALTEFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMA 300

Query: 296 PEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDL 355
           PEYGATAAMFFID+QT+DYLRLTGR+DEQ++LVETYA+ AGLWAD+L  A+YER L FDL
Sbjct: 301 PEYGATAAMFFIDDQTLDYLRLTGRSDEQVRLVETYAKAAGLWADTLAAAQYERTLSFDL 360

Query: 356 SSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTS 415
           SSVVRNMAGPSNPHKRLPT+ LA RGIA        QE  G MPDGAVIIAAITSCTNTS
Sbjct: 361 SSVVRNMAGPSNPHKRLPTADLAARGIA-----GQWQEQPGQMPDGAVIIAAITSCTNTS 415

Query: 416 NPRNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAF 475
           NPRNVIAAALLARNANARGL RKPWVKSSLAPGSKAVELYL+EANLLP+LEKLGFGIVAF
Sbjct: 416 NPRNVIAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLLPELEKLGFGIVAF 475

Query: 476 ACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535
           ACTTCNGMSGALDP IQQEI++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA
Sbjct: 476 ACTTCNGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535

Query: 536 IAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITA 595
           IAGTIRFDIE+DVLG D +G+PV LKDIWPSDEEID IVA SVKPEQFRKVYEPMFA T 
Sbjct: 536 IAGTIRFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFARTG 595

Query: 596 ASGESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIM 655
            SG   +PLYDWR QSTYIRRPPYWEGALAGERTLK +R LAVLGDNITTDHLSPSNAIM
Sbjct: 596 RSGTRAAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIM 655

Query: 656 LNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLAR 715
            +SAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTL+NEMAVVDG+VKKGSLAR
Sbjct: 656 ADSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLAR 715

Query: 716 IEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFER 775
           +EPEGKV+RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAGVE I AEGFER
Sbjct: 716 VEPEGKVMRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFER 775

Query: 776 IHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVP 835
           IHRTNLIGMGVLPLEF+PG +R TLG+DGTET+DV G R PRA LTLV++R+NGERVEVP
Sbjct: 776 IHRTNLIGMGVLPLEFQPGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVP 835

Query: 836 VTCRLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           VTCRLD+ EEVSIYEAGGVL  FAQDFLE+++A
Sbjct: 836 VTCRLDTAEEVSIYEAGGVLQRFAQDFLEAAQA 868


Lambda     K      H
   0.318    0.135    0.398 

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: 2239
Number of extensions: 86
Number of successful extensions: 4
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: 869
Length of database: 869
Length adjustment: 42
Effective length of query: 827
Effective length of database: 827
Effective search space:   683929
Effective search space used:   683929
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: 56 (26.2 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