Alignments for a candidate for acnD in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Ochrobactrum thiophenivorans DSM 7216

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_094506127.1 CEV31_RS06075 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_002252445.1:WP_094506127.1
          Length = 895

 Score =  704 bits (1818), Expect = 0.0
 Identities = 394/898 (43%), Positives = 550/898 (61%), Gaps = 44/898 (4%)

Query: 1   MSTVMNTQYRKPLP--GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVR------- 51
           MS + + + RK L   G    Y+   EA +    G  +KLP++ +VL ENL+R       
Sbjct: 1   MSHIDSFKCRKTLTVGGKEYVYYSLTEAEKNGLTGV-SKLPFSMKVLLENLLRFEDDRTV 59

Query: 52  -RCEPEMLTASLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPA 110
            + + E + A L     +  E+ +   PARV+  D  G  A+VDLA +RD + A GGDP 
Sbjct: 60  KKSDIEAIAAWLNDRGSAGAEIAYR--PARVLMQDFTGVPAVVDLAAMRDGLKALGGDPE 117

Query: 111 QVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIP 170
           ++NP+VP  L++DHS+ V+  G +  AF  N  +E +RN +R+ F+ W Q+AFKN  V+P
Sbjct: 118 KINPLVPVDLVIDHSVIVDEFG-NPSAFKANVDLEYQRNGERYRFLKWGQQAFKNFRVVP 176

Query: 171 QGNGIMHQINLERMSPVIHARNG----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAE 226
            G GI HQ+NLE ++  +  +      VA+PDT VGTDSHT  V+ LGV+  GVGG+EAE
Sbjct: 177 PGTGICHQVNLEYLAQAVWTKEEDGETVAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAE 236

Query: 227 SVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEA 286
           + MLG+   M LP++IG  LTGK + G+TATD+VL +T+ LR + VV  ++EFFGEG + 
Sbjct: 237 AAMLGQPVSMLLPEVIGFRLTGKVKEGVTATDLVLTVTQMLRKKGVVGKFVEFFGEGLDN 296

Query: 287 LTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSD-D 345
           +TL DRATI+NM PE+GAT   F ID +TL+Y+  TGR  +++ LVE Y++  G+W +  
Sbjct: 297 MTLADRATIANMGPEYGATCGFFPIDNETLNYMNTTGRAEDRMALVEAYSRAQGMWREAG 356

Query: 346 LKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAA----------RGISGE-----V 390
            +  V+   L  D+S VV ++AGP  P  R+    + +          +  +G+     V
Sbjct: 357 SEDPVFTDILELDMSEVVPSMAGPKRPEGRIALENIGSGFATSLETEYKKTTGQAARYAV 416

Query: 391 ENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKA 450
           E E   +  G V IAAITSCTNTSNP  +IAAGLLARNA AKGL  KPWVKTSLAPGS+ 
Sbjct: 417 EGEDFDLGHGDVAIAAITSCTNTSNPSVLIAAGLLARNAVAKGLKTKPWVKTSLAPGSQV 476

Query: 451 VQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRN 510
           V  YLE A L  +L++LGF +VGF CTTC G SG L   I + + ++ L A AVLSGNRN
Sbjct: 477 VAAYLESAGLQKDLDALGFNLVGFGCTTCIGNSGPLPAPISKTINEKGLIAAAVLSGNRN 536

Query: 511 FDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEID 570
           F+GR+ P  +  +LASPPLVVA+A+AGT+  D+ K+ LG D++G PV L +IWPS AEI 
Sbjct: 537 FEGRVSPDVQANYLASPPLVVAHALAGTVTKDLTKEPLGEDQNGNPVFLRDIWPSSAEIQ 596

Query: 571 AVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEGALAGER 627
             IA +V  + F + Y  +F    ++     P    Y W   STY++ PPY+ G      
Sbjct: 597 EFIAKNVTRKIFSEKYADVFKGDENWQAVQVPAGQTYAWDDNSTYVQNPPYFVGMGKSAG 656

Query: 628 TL---KGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHL 684
           T+   KG R L + GD ITTDH+SP+ +I   S AG+YL   G+   DFN Y T RG+H 
Sbjct: 657 TIADVKGARVLGLFGDKITTDHISPAGSIKAQSPAGKYLIDHGVGIADFNQYGTRRGNHE 716

Query: 685 TAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGA 744
              R TFAN +++N M   +G  ++G      P    T +++A   Y     PL++ AG 
Sbjct: 717 VMMRGTFANIRIRNHMLGENG--REGGYTIHYPSKEETSIYDAAMQYKAEGVPLVVFAGV 774

Query: 745 DYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGT 804
           +YG GSSRDWAAKG  L GV+A++A+ FERIHR+NLVGMG++P  F+ G +  T G+ G 
Sbjct: 775 EYGNGSSRDWAAKGTNLLGVKAVIAQSFERIHRSNLVGMGIVPFVFEEGTSWQTLGLKGD 834

Query: 805 EVFDVIG--SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQD 860
           E+  + G   + PR  +   IT  +G   +VP+ CR+DT +E+   + GG+LQ   +D
Sbjct: 835 EIVSIEGLADVRPRQKIEASITFADGSVKKVPLICRIDTLDELDYMKNGGILQTVLRD 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: 1941
Number of extensions: 104
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: 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 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