Alignments for a candidate for acnD in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Magnetospirillum magneticum AMB-1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000009985.1:WP_011386009.1
          Length = 903

 Score =  677 bits (1746), Expect = 0.0
 Identities = 381/876 (43%), Positives = 527/876 (60%), Gaps = 41/876 (4%)

Query: 26  AIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-LKQII----ESKQELDFPWFPAR 80
           A++A+  G  ++LP + R++ E+++R C+ + +T   ++Q+     ++ +  + P+  AR
Sbjct: 27  ALDAVTDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLANWRPDAPRTQEIPFVVAR 86

Query: 81  VVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAK 140
           +V  D  G   L DLA +R    A G +P  + P+VP  L+VDHS+ V++ G + D+   
Sbjct: 87  IVLQDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVVDHSVQVDHYG-EADSLDL 145

Query: 141 NRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTL 200
           N   E +RN +R+ FI W  +AF    V+P G GI+HQ+NLE ++  +  ++G+ +PDTL
Sbjct: 146 NMRREFQRNAERYRFIKWGMQAFDTFRVVPPGIGIVHQVNLEFLARGVLEKDGITYPDTL 205

Query: 201 VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIV 260
           VGTDSHT  ++ALGV   GVGG+EAE+ MLG+      PD++GV L G+   G TATD+V
Sbjct: 206 VGTDSHTTMINALGVAGWGVGGIEAEAGMLGQPLVFLTPDVVGVHLHGRLPEGATATDLV 265

Query: 261 LALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLT 320
           L LTE LR  KVV  ++EFFGEG  +L + DRATI+NM PE+GAT   F +D++T+ YL 
Sbjct: 266 LFLTERLRRAKVVGKFVEFFGEGTRSLAVPDRATIANMAPEYGATMGFFPVDKETVRYLE 325

Query: 321 LTGREAEQVKLVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVRTIAGPSNPHARVPTS 379
            TGR   ++++   Y    GL+   +   + Y   + FDL SV  +IAGP  P  R+  S
Sbjct: 326 ATGRTDSEIEVFRAYYSAQGLFGMPMPGDIDYSEVIEFDLGSVQPSIAGPKRPQDRLNLS 385

Query: 380 EL---------------------AARGISGEVENEPGL-MPDGAVIIAAITSCTNTSNPR 417
           ++                      A G    VE      +  G V+IAAITSCTNTSNP 
Sbjct: 386 DMRRAFTSLFSAPAKDDGYGRPAEALGRRHRVETTAAADIGHGDVLIAAITSCTNTSNPG 445

Query: 418 NVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACT 477
            ++AAGLLAR A A GL   P VKTSLAPGS+ V  YL +A LL +LESLGFG+V + CT
Sbjct: 446 VMLAAGLLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKAGLLGDLESLGFGVVAYGCT 505

Query: 478 TCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 537
           TC G SG L P ++Q +   DL   AVLSGNRNF+ RIHP  K  FL SPPLVVA+AIAG
Sbjct: 506 TCIGNSGPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPAIKANFLMSPPLVVAFAIAG 565

Query: 538 TIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF---DLSV 594
            I  D+ ++ LG  KDGKPV L +IWPS  E+   +  +  PE +R++Y        L  
Sbjct: 566 RIAIDMTQEPLGTGKDGKPVMLKDIWPSGREVADALLVATDPELYRRLYSDFVHGNPLWN 625

Query: 595 DYGDKVSPLYDWRPQSTYIRRPPYWE---GALAGERTLKGMRPLAVLGDNITTDHLSPSN 651
           D   +  P Y W   STYI  PP++E      AG   + G R LA+ GD++TTDH+SP+ 
Sbjct: 626 DIPTQTGPAYAWE-TSTYIAEPPFFERFSPQPAGVGDIIGARALAIFGDSVTTDHISPAG 684

Query: 652 AIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQ 709
           +I + S AG+YL   G+   DFNSY   RG+H    R TFAN +++N M  A VDG   +
Sbjct: 685 SIAVSSPAGQYLLAHGVAAGDFNSYGARRGNHEVMMRGTFANVRIRNLMLPAKVDGSRVE 744

Query: 710 GSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVA 769
           G L   +PEG    +++A   Y +   P I+ AG +YG GSSRDWAAKG +L GV A+VA
Sbjct: 745 GGLTLHQPEGSEMPIFDAASRYQEAGIPSIVFAGTEYGTGSSRDWAAKGPKLLGVRAVVA 804

Query: 770 EGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDV---IGSIAPRADLTVIITRK 826
           + FERIHR+NLVGMGVLPL+F+ GE+ A+ GI G E F V    G + PR ++ + I  +
Sbjct: 805 QSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFHVRGLSGVLRPRQEVVLEIVNR 864

Query: 827 NGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFL 862
            G    + +  R+DTA E+     GG+L    +D L
Sbjct: 865 QGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLL 900


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: 1952
Number of extensions: 96
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 867
Length of database: 903
Length adjustment: 43
Effective length of query: 824
Effective length of database: 860
Effective search space:   708640
Effective search space used:   708640
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