Alignments for a candidate for acnD in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Mesorhizobium ciceri WSM1271

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate YP_004140183.1 Mesci_0969 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000185905.1:YP_004140183.1
          Length = 896

 Score =  709 bits (1831), Expect = 0.0
 Identities = 391/880 (44%), Positives = 542/880 (61%), Gaps = 38/880 (4%)

Query: 15  GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII------ES 68
           G    YFD  EA +    G  ++LPY+ +VL ENL+R  +   +T    Q +      + 
Sbjct: 18  GAEYAYFDLIEAEKNGLTGI-SQLPYSMKVLLENLLRNEDGRSVTKESIQAVAGWLTDKG 76

Query: 69  KQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAV 128
              ++  + PARV+  D  G  A+VDLA +RDA+A+ GGDP ++NP+VP  L++DHS+ V
Sbjct: 77  TAGVEIAYRPARVLMQDFTGVPAVVDLAAMRDAMASLGGDPQKINPLVPVDLVIDHSVIV 136

Query: 129 EYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVI 188
           +  G    AFA+N  +E  RNE+R+ F+ W Q+AF+N  V+P G GI HQ+NLE +  V+
Sbjct: 137 DEFGTPM-AFARNVELEYERNEERYKFLKWGQQAFRNFRVVPPGTGICHQVNLEYLGQVV 195

Query: 189 --HARNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
             +  +G   A+PDT VGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M LP++IG 
Sbjct: 196 WTNTEDGETTAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLLPEVIGF 255

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
            LTGK + G+TATD+VL +T+ LR + VV  ++EFFG G   +TL DRATI NM PE+GA
Sbjct: 256 RLTGKLKEGVTATDLVLTVTQMLRKKGVVGKFVEFFGPGLSNMTLADRATIGNMAPEYGA 315

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDD-LKQAVYPRTLHFDLSSVV 363
           T   F +D +T+ YLT++GR  +++ LVE YAK  GLW +      V+   L  +L SVV
Sbjct: 316 TCGFFPVDSETIRYLTMSGRSEDRIALVEAYAKAQGLWRETGSADPVFTDLLELELGSVV 375

Query: 364 RTIAGPSNPHARVPTSELA---ARGISGE------------VENEPGLMPDGAVIIAAIT 408
            ++AGP  P  RV    +    A+ +  E            VE     +  G V+IAAIT
Sbjct: 376 PSMAGPKRPEGRVALEGIPEGFAKAMETEYKKAAEISKRYAVEGTDHDLGHGDVVIAAIT 435

Query: 409 SCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLG 468
           SCTNTSNP  +I AGLLARNAN  GL +KPWVKTSLAPGS+ V  YLE++ L  EL+ +G
Sbjct: 436 SCTNTSNPSVLIGAGLLARNANRLGLKQKPWVKTSLAPGSQVVAEYLEKSGLQKELDQIG 495

Query: 469 FGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPP 528
           F +VGF CTTC G SG L   I + + D+ L A AVLSGNRNF+GR+ P  +  +LASPP
Sbjct: 496 FNLVGFGCTTCIGNSGPLPAPISKTINDKGLIAAAVLSGNRNFEGRVSPDVQANYLASPP 555

Query: 529 LVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEP 588
           LVVA+A+AGT+  D+  + LG DK+G+PV L +IWPS AEI   I  +V  E F + Y  
Sbjct: 556 LVVAHALAGTVTKDLTTEPLGEDKNGEPVYLKDIWPSSAEIQEFIEKNVTRELFARKYAD 615

Query: 589 MFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEGALAG---ERTLKGMRPLAVLGDNI 642
           +F     + +  +P    Y W   STY++ PPY+ G  +G      +KG R L + GD I
Sbjct: 616 VFKGDEYWQNVKAPEGQTYAWDDNSTYVQNPPYFAGMTSGFGKIGDIKGARVLGLFGDKI 675

Query: 643 TTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAI 702
           TTDH+SP+ +I   S AG+YL   G+   DFN Y T RG+H    R TFAN +++N M  
Sbjct: 676 TTDHISPAGSIKAASPAGKYLTDHGVGVADFNQYGTRRGNHEVMMRGTFANIRIRNHMLG 735

Query: 703 VDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLA 762
            +G  ++G      P      +++A   Y     PL++ AG +YG GSSRDWAAKG  L 
Sbjct: 736 ENG--REGGYTIHYPSKEEESIYDAAMEYKREGVPLVVFAGVEYGNGSSRDWAAKGTNLL 793

Query: 763 GVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAPRADLT 820
           GV A++A+ FERIHR+NLVGMGV+P  F+ G + A+  + G E+ ++ G  +I PR  + 
Sbjct: 794 GVRAVIAQSFERIHRSNLVGMGVIPFVFEEGTSWASLNLKGDELVEIDGLSTIKPRQTMI 853

Query: 821 VIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQD 860
             IT  +G    VP+ CR+DT +E+  ++ GG+LQ   +D
Sbjct: 854 AKITYGDGTVKNVPIICRIDTLDELDYFKNGGILQYVLRD 893


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: 1993
Number of extensions: 111
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: 896
Length adjustment: 43
Effective length of query: 824
Effective length of database: 853
Effective search space:   702872
Effective search space used:   702872
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