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_035237830.1 Q366_RS07760 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000745975.1:WP_035237830.1
          Length = 895

 Score =  678 bits (1750), Expect = 0.0
 Identities = 377/879 (42%), Positives = 532/879 (60%), Gaps = 51/879 (5%)

Query: 25  EAIEAIAPGAYAKLPYTSRVLAENLVRRCE-----PEMLTASLKQIIESKQELDFPWFPA 79
           E +E    G  ++LP++ ++L E  +R  +      + + A      + K E + P+ P 
Sbjct: 25  ENLEKQGIGHISRLPFSIKILLEQALRNLDHFQVNEDDIVALANWQPKQKSEKEIPFKPT 84

Query: 80  RVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFA 139
           RV+  D+ G  ALVDLA LR +++  GG+PA +NP +P  LI+DHS+ V+  G   D+  
Sbjct: 85  RVILQDLTGVPALVDLAALRTSMSQLGGNPAVINPKIPVDLIIDHSIQVDSFGMP-DSLQ 143

Query: 140 KNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDT 199
            N   E  RN +R+ F+ W QK FKN+ + P G GI+HQ+NLE ++ V+  R  + F DT
Sbjct: 144 INMEKEFERNRERYEFLKWGQKNFKNMKIFPPGVGIVHQVNLESLANVVQMRENICFSDT 203

Query: 200 LVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDI 259
           +VGTDSHTP V++LGV+  GVGG+EAESVMLG+  YM++P ++G +LTGK  PG TATD+
Sbjct: 204 VVGTDSHTPMVNSLGVLGWGVGGIEAESVMLGQPIYMQIPQVVGFKLTGKMSPGTTATDL 263

Query: 260 VLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYL 319
           V  + + LR   VV  ++EF+G+G   L+L DRATISNM PE+GAT   F  D +TL YL
Sbjct: 264 VFRIVQILRQVGVVEKFVEFYGDGLSGLSLADRATISNMAPEYGATMGFFPTDTETLRYL 323

Query: 320 TLTGREAEQVKLVETYAKTAGLW-SDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPT 378
             TGR  E ++ VE Y K  GL+ +D +    +   +  DLS+V  ++AGP  P  R+  
Sbjct: 324 KGTGRSPEVIERVEHYCKAQGLFRTDGMSAPEFSDDIELDLSTVEPSLAGPKRPQDRIGL 383

Query: 379 SELA---ARGISGEV--------ENE--------------PGLMPDGAVIIAAITSCTNT 413
           S++    A+ ++  V        ENE              P ++  G+V++AAITSCTNT
Sbjct: 384 SDMKHAWAKSLTAPVSQRGYELKENELSAQAEIRLPESEKPFVLAHGSVVLAAITSCTNT 443

Query: 414 SNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVG 473
           SNP  +IAAGLLAR A  KGL  KPWVKTSLAPGS+ V  YL +A L   LE LGF  VG
Sbjct: 444 SNPSVMIAAGLLARKAVEKGLKTKPWVKTSLAPGSRVVTDYLHQAKLDSFLEQLGFFTVG 503

Query: 474 FACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAY 533
           + CT+C G SG L   +   VID+DL   +VLSGNRNF+GR++P  K  +LASPPLVVAY
Sbjct: 504 YGCTSCIGNSGPLPEPVSDAVIDKDLVVASVLSGNRNFEGRVNPLTKANYLASPPLVVAY 563

Query: 534 AIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLS 593
           AI GT+  ++ +D LG D +G PV L +IWP  +EI A I A + PE + K Y     LS
Sbjct: 564 AITGTVNINLLEDPLGTDPNGHPVYLKDIWPDPSEI-AEITALITPEMYLKRYSNFETLS 622

Query: 594 VDYGD---KVSPLYDWRPQSTYIRRPPYW---EGALAGERTLKGMRPLAVLGDNITTDHL 647
             + +   K   +Y W   STYIR PP++     AL   R +   + L  +GD++TTDH+
Sbjct: 623 PLWNEIPTKGDEVYAWDQSSTYIRNPPFFLNMSKALKPIRDIVDAKVLVKVGDSVTTDHI 682

Query: 648 SPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKV 707
           SP+ AI  +S A  YL +  + + DFNSY + RG+     R TFAN +L+N++A      
Sbjct: 683 SPAGAISKNSPAAAYLLEHEIQQADFNSYGSRRGNDQVMVRGTFANIRLRNQLA----PG 738

Query: 708 KQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI 767
            +G +    P G    +++A E Y     PLI++AG +YG GSSRDWAAKG  L GV+A+
Sbjct: 739 TEGGITTYLPTGEQMSIFDASEKYKASGTPLIVLAGREYGTGSSRDWAAKGTYLLGVKAV 798

Query: 768 VAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLTVIIT 824
           +A  +ERIHR+NL+GMGVLPL+FK   +  +  + G E + ++G    I P  +LT+ + 
Sbjct: 799 IATSYERIHRSNLLGMGVLPLQFKDSNSPDSLNLTGKESYSILGLSDEIKPGQELTLKVD 858

Query: 825 RKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863
            +     E+ V  RLDT  E+  Y+ GG+L    ++F++
Sbjct: 859 DR-----EIAVVLRLDTPVEIEYYQNGGILHTVLRNFIK 892


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: 1906
Number of extensions: 77
Number of successful extensions: 8
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: 895
Length adjustment: 43
Effective length of query: 824
Effective length of database: 852
Effective search space:   702048
Effective search space used:   702048
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