Alignments for a candidate for acnD in Rhodopseudomonas pseudopalustris DSM 123

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Rhodopseudomonas pseudopalustris DSM 123

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_092685791.1 BMY71_RS19130 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_900110435.1:WP_092685791.1
          Length = 905

 Score =  701 bits (1808), Expect = 0.0
 Identities = 386/863 (44%), Positives = 533/863 (61%), Gaps = 47/863 (5%)

Query: 36  AKLPYTSRVLAENLVRRCEPEM-----LTASLKQIIESKQELDFPWFPARVVCHDILGQT 90
           ++LPY+ +VL ENL+R  +        + A  K + +   E +  + PARV+  D  G  
Sbjct: 37  SRLPYSMKVLLENLLRNEDDRTVKKADIQAVAKWMRKKALEHEIAFRPARVLMQDFTGVP 96

Query: 91  ALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNE 150
           A+VDLA +R+A+ A GGD  ++NP+VP  L++DHS+ V + G D  AF KN A E ++N+
Sbjct: 97  AVVDLAAMRNAMQALGGDAEKINPLVPVDLVIDHSVIVNFFG-DNKAFGKNVAEEYKQNQ 155

Query: 151 DRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG------------VAFPD 198
           +R+ F+ W QKAF N  V+P G GI HQ+NLE ++  +  R              VA+PD
Sbjct: 156 ERYEFLKWGQKAFSNFAVVPPGTGICHQVNLEYLAQTVWTRKEKMTIGKKKGTFEVAYPD 215

Query: 199 TLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATD 258
           +LVGTDSHT  V+ L V+  GVGG+EAE+ MLG+   M LP+++G +L G  + G+TATD
Sbjct: 216 SLVGTDSHTTMVNGLAVLGWGVGGIEAEAAMLGQPLSMLLPEVVGFKLKGALKEGVTATD 275

Query: 259 IVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDY 318
           +VL +T+ LR Q VV  ++EFFG G + L++ D++TI+NM PE+GAT   F +D +TLDY
Sbjct: 276 LVLTVTQMLRKQGVVGKFVEFFGPGLDHLSVADKSTIANMAPEYGATCGFFPVDTETLDY 335

Query: 319 LTLTGREAEQVKLVETYAKTAGLW-SDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVP 377
           L  +GR + +V LVE YAK  GL+ +      V+  TL  DL+SVV ++AGP  P  RV 
Sbjct: 336 LKTSGRASARVALVEKYAKAQGLFRTAKSADPVFTVTLTLDLASVVPSLAGPKRPEGRVA 395

Query: 378 TSELAARGISGEVENEPGLMPDGA---------------VIIAAITSCTNTSNPRNVIAA 422
              ++  G +  ++ E     DGA               V+IAAITSCTNTSNP  +I A
Sbjct: 396 LPTVS-EGFTAAMDAEYKKALDGARYAVDGRKFDLGHGDVVIAAITSCTNTSNPSVLIGA 454

Query: 423 GLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGM 482
           GLLARNA AKGL   PWVKTSLAPGS+ V  YL  + L  +L+ +GF +VGF CTTC G 
Sbjct: 455 GLLARNAAAKGLKAAPWVKTSLAPGSQVVAEYLANSGLQKDLDKVGFNLVGFGCTTCIGN 514

Query: 483 SGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFD 542
           SG L   I + + D  + A AVLSGNRNF+GR+ P  +  +LASPPLVVAYA+AGT+  +
Sbjct: 515 SGPLPEDISKSINDNGIVAAAVLSGNRNFEGRVSPDVQANYLASPPLVVAYALAGTVTKN 574

Query: 543 IEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV-- 600
           +  + +G  KDGKPV L +IWP+  EI+A +   V    F+K Y  +F    ++  K+  
Sbjct: 575 LAVEPIGTGKDGKPVYLKDIWPTTKEINAFVKKYVTAAIFKKKYADVFKGDTNW-RKIKT 633

Query: 601 --SPLYDWRPQSTYIRRPPYWEGALAGERTLKGM---RPLAVLGDNITTDHLSPSNAIMM 655
             S  Y W   STY++ PPY+EG       +  +   R LAV GD ITTDH+SP+ +I +
Sbjct: 634 VDSETYKWNMSSTYVQNPPYFEGMKMQPEPIVDVVDARILAVFGDKITTDHISPAGSIKL 693

Query: 656 DSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAI-VDGKVKQGSLAR 714
            S AG+YL +  +   DFN Y T RG+H    R TFAN ++KN M    DG + +G L +
Sbjct: 694 TSPAGKYLSEHQVRPADFNQYGTRRGNHEVMMRGTFANIRIKNHMLKGADGNIPEGGLTK 753

Query: 715 IEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFER 774
             P+G    +++A   Y   + PL++ AGA+YG GSSRDWAAKG RL GV A++ + FER
Sbjct: 754 HWPDGDQMSIYDAAMKYQAEQVPLVVFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFER 813

Query: 775 IHRTNLVGMGVLPLEFKAGENRATYGIDGTE---VFDVIGSIAPRADLTVIITRKNGERV 831
           IHR+NLVGMGVLPL F+ G + A+ GI G E   +  + G + PR  LT  I   NG+  
Sbjct: 814 IHRSNLVGMGVLPLTFEDGTSWASLGIKGDEKVTIRGLQGDLKPRQTLTAEIKAGNGKVK 873

Query: 832 EVPVTCRLDTAEEVSIYEAGGVL 854
            VP+ CR+DT +E+  Y  GG+L
Sbjct: 874 RVPLLCRIDTLDELEYYRNGGIL 896


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: 1929
Number of extensions: 98
Number of successful extensions: 10
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: 905
Length adjustment: 43
Effective length of query: 824
Effective length of database: 862
Effective search space:   710288
Effective search space used:   710288
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 24 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