Alignments for a candidate for acnD in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Sinorhizobium meliloti 1021

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate SMc03846 SMc03846 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Smeli:SMc03846
          Length = 896

 Score =  707 bits (1826), Expect = 0.0
 Identities = 391/887 (44%), Positives = 544/887 (61%), Gaps = 40/887 (4%)

Query: 10  RKPLPGTALDY-FDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII-- 66
           R  L    +DY + +    EA      +KLPY+ +VL ENL+R  +   +T    + I  
Sbjct: 11  RSTLTVNGVDYVYYSLPKAEANGLAGISKLPYSMKVLLENLLRNEDGRSVTKKDIENIAA 70

Query: 67  ----ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIV 122
               +   E +  + PARV+  D  G  A+VDLA +RDA+ + GGDP ++NP+VP  L++
Sbjct: 71  WLGDKGTAENEIAYRPARVLMQDFTGVPAVVDLAAMRDAMVSLGGDPEKINPLVPVDLVI 130

Query: 123 DHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLE 182
           DHS+ V+  G    AFA+N  +E +RN +R+ F+ W Q+AFKN  V+P G GI HQ+NLE
Sbjct: 131 DHSVIVDEFG-TPTAFARNVELEYQRNGERYRFLKWGQQAFKNFRVVPPGTGICHQVNLE 189

Query: 183 RMSPVIHARNG----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRL 238
            +   +  R       A+PDT VGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M L
Sbjct: 190 YLGQAVWTREEDGEVTAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLL 249

Query: 239 PDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNM 298
           P++IG +LTGK + G+TATD+VL + + LR + VVS ++EFFG G + +TL DRATI NM
Sbjct: 250 PEVIGFKLTGKLKEGVTATDLVLTVVQMLRKKGVVSKFVEFFGPGLDNMTLADRATIGNM 309

Query: 299 TPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSD-DLKQAVYPRTLHF 357
            PE+GAT   F +D +T++YLT++GRE +++ LVE Y+K  G+W + D  + V+  TL  
Sbjct: 310 GPEYGATCGFFPVDAETINYLTISGREEQRIALVEAYSKAQGMWREGDGSELVFTDTLEL 369

Query: 358 DLSSVVRTIAGPSNPHARVPTSELAARGISGEVENE---PGLMPD-------------GA 401
           DL  VV ++AGP  P  R+    +A+ G +  ++N+   PG + +             G 
Sbjct: 370 DLGDVVPSMAGPKRPEGRIALENIAS-GFAAALDNDYKKPGQLANRYAVEGTDYDLGHGD 428

Query: 402 VIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLL 461
           V IAAITSCTNTSNP  +IAAGLLARNA AKGL  +PWVKTSLAPGS+ V  YL ++ L 
Sbjct: 429 VAIAAITSCTNTSNPSVLIAAGLLARNAVAKGLKTQPWVKTSLAPGSQVVAEYLSKSGLQ 488

Query: 462 PELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQ 521
            +L+ LGF +VGF CTTC G SG L   I + + D+ L A  VLSGNRNF+GRI P  + 
Sbjct: 489 TDLDKLGFNLVGFGCTTCIGNSGPLPTEISKTINDKGLIAAGVLSGNRNFEGRISPDVQA 548

Query: 522 AFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQ 581
            +LASPPLVVAYA+AG+++ D+ K+ +G D+DG+PV L +IWP+  EI   I   V  E 
Sbjct: 549 NYLASPPLVVAYALAGSVQKDLTKEPIGEDRDGQPVYLRDIWPTSQEIQDFIFRYVTREL 608

Query: 582 FRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPL 635
           +   Y  +F    ++     P    Y W   STY++ PPY+ G     AG   +K  R L
Sbjct: 609 YATKYADVFKGDANWQAVQVPAGQTYAWDEGSTYVQNPPYFVGMGKKGAGISDIKNARVL 668

Query: 636 AVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPK 695
            + GD ITTDH+SP+ +I   S AG YL + G+   DFN Y T RG+H    R TFAN +
Sbjct: 669 GLFGDKITTDHISPAGSIKAASPAGAYLLEHGVGIADFNQYGTRRGNHEVMMRGTFANIR 728

Query: 696 LKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWA 755
           ++N M   +G  K+G      P      +++A   Y +   PL+I AG +YG GSSRDWA
Sbjct: 729 IRNHMLGPNG--KEGGYTIHYPSKEEMSIYDAAMQYKEEGVPLVIFAGVEYGNGSSRDWA 786

Query: 756 AKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDV--IGSI 813
           AKG  L GV+A++A+ FERIHR+NLVGMGV+P  F+ G    + G+ G EV  +  + ++
Sbjct: 787 AKGTNLLGVKAVIAQSFERIHRSNLVGMGVVPFVFEEGMTWESLGLKGDEVVTIENLANV 846

Query: 814 APRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQD 860
            PR      IT  +G   EVP+ CR+DT +EV+    GG+LQ   +D
Sbjct: 847 QPREKRVAKITYGDGSVKEVPLICRIDTLDEVTYVNNGGILQTVLRD 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: 1948
Number of extensions: 97
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: 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 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