Alignments for a candidate for acnD in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Desulfobacter vibrioformis DSM 8776

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_084691817.1 Q366_RS12560 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000745975.1:WP_084691817.1
          Length = 897

 Score =  696 bits (1795), Expect = 0.0
 Identities = 381/862 (44%), Positives = 535/862 (62%), Gaps = 44/862 (5%)

Query: 27  IEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIESKQ-------ELDFPWFPA 79
           +E+ A    A+LP++ RVL ENL+R+       A  K ++ + Q        ++ P++PA
Sbjct: 35  LESKAGIPLARLPFSIRVLVENLLRKVASG--EAKAKDVLAAAQWQPSYDDSVEIPFYPA 92

Query: 80  RVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFA 139
           RV+  D  G  A+VDLA +RDA+AA G DPA VNP++P +LIVDHS+ V++ G  +    
Sbjct: 93  RVLMQDFTGVPAVVDLAAMRDAMAAAGKDPALVNPLIPVELIVDHSVQVDFNG-TQACRQ 151

Query: 140 KNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR----NGVA 195
           KN A E  RN +R+  + W QK+F N  V+P  +GI HQ+NLE +           + + 
Sbjct: 152 KNVAKEYERNGERYRLLKWAQKSFDNFRVVPPNSGICHQVNLEYLGRCAMREKTQTHDLL 211

Query: 196 FPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGIT 255
           F DTLVGTDSHTP ++++GV+  GVGG+EAE+VMLG+  +M LP +IGVELTG+  PG+T
Sbjct: 212 FADTLVGTDSHTPMINSIGVLGWGVGGIEAEAVMLGQPYFMPLPQVIGVELTGRLNPGVT 271

Query: 256 ATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQT 315
           ATD+VL +T  LR   VV  ++EF+G G + L + DRATI+NM+PE+GAT   F ID+QT
Sbjct: 272 ATDMVLTVTNRLRQMNVVEKFVEFYGSGLKNLKVPDRATIANMSPEYGATMGFFPIDEQT 331

Query: 316 LDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHAR 375
           +DY  +T R  EQ ++VE +AK  GL+ +D     +  +L  DL+ +V  +AGP+ P   
Sbjct: 332 IDYFRITNR-GEQGEVVEAWAKACGLFRNDGDIPEFSDSLKIDLTEIVPCLAGPARPQDL 390

Query: 376 VPTSELAA-------------RGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAA 422
           V   +L               + I+  + + P  + +G+V+IAAITSCTNTSNP  ++ A
Sbjct: 391 VKLGDLKTNFSGLLDATAPENKQINIRLNDTPAQIGNGSVVIAAITSCTNTSNPYVLLGA 450

Query: 423 GLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGM 482
           GLLARNA  KG+  KP VKTS APGSK V  YL +A L+P LESLGF +  F CTTC G 
Sbjct: 451 GLLARNAVKKGIFPKPHVKTSFAPGSKVVVDYLSDAGLMPYLESLGFHVAAFGCTTCIGN 510

Query: 483 SGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFD 542
           SG L P I++++ ++DL   AVLSGNRNF+ RIH   K  FLASP LVVA+A+ G +  +
Sbjct: 511 SGPLHPEIEKQIKEKDLAVAAVLSGNRNFEARIHQLTKANFLASPMLVVAFALCGRVDVN 570

Query: 543 IEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFD-----LSVDYG 597
           +EK+ + LD +G+PV L  IWP D EI+ ++   VK E F+  YE +F       ++D  
Sbjct: 571 LEKEPVALDPNGEPVYLKEIWPGDDEIEDLVHRHVKKEDFQNQYEQIFQGDNFWKALDIT 630

Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGM---RPLAVLGDNITTDHLSPSNAIM 654
             V+  + W P+STYIR PPY+E      ++L+     R L  LGD++TTDH+SP+ AI 
Sbjct: 631 QSVT--FSWDPESTYIRNPPYFENFSLSPKSLENFEDARALMTLGDSVTTDHISPAGAIP 688

Query: 655 MDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLAR 714
               AG YL + G+  + FNSY   RG+H    R TF N ++KN+M       K+GS  +
Sbjct: 689 EHYPAGIYLKEQGIDADSFNSYGARRGNHEVMMRGTFGNIRIKNQMV----TPKEGSFTK 744

Query: 715 IEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFER 774
             P+G    +++  ++Y   + PLI++AG +YG GSSRDWAAKG  L GV A++A  +ER
Sbjct: 745 EFPQGGTGFVFDVAKSYGQHQVPLIVLAGKEYGTGSSRDWAAKGSALLGVRAVIARSYER 804

Query: 775 IHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAPRADLTVIITRKNGERVE 832
           IHR+NLVGMGVLPL+F  G+     G+DG+E+F V G   + P  +L V   + +G  V 
Sbjct: 805 IHRSNLVGMGVLPLQFLDGDGWQELGLDGSELFSVKGMAQLTPHKELQVTAQKADGSEVT 864

Query: 833 VPVTCRLDTAEEVSIYEAGGVL 854
                RLDT  +V     GG+L
Sbjct: 865 FKAIARLDTDIDVEYMIHGGIL 886


Lambda     K      H
   0.318    0.136    0.397 

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: 1920
Number of extensions: 82
Number of successful extensions: 11
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: 867
Length of database: 897
Length adjustment: 43
Effective length of query: 824
Effective length of database: 854
Effective search space:   703696
Effective search space used:   703696
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 Apr 09 2024. 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 2024 update 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