Alignments for a candidate for acnD in Rhizobium etli CFN 42

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Rhizobium etli CFN 42

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_011427135.1 RHE_RS20170 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000092045.1:WP_011427135.1
          Length = 896

 Score =  694 bits (1792), Expect = 0.0
 Identities = 386/876 (44%), Positives = 535/876 (61%), Gaps = 40/876 (4%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII------ESKQELD 73
           Y+   +A     PG  +KLPY+ +VL ENL+R  + + +T      +      +   E +
Sbjct: 23  YYSLPKAEANGLPGV-SKLPYSMKVLLENLLRFEDGQSVTKEHILAVAAWLNNKGAVENE 81

Query: 74  FPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGF 133
             + PARV+  D  G  A+VDLA +RDA+ + GGDP ++NP+VP  L++DHS+ V+  G 
Sbjct: 82  IAYRPARVLMQDFTGVPAVVDLAAMRDAMVSLGGDPEKINPLVPVDLVIDHSVIVDEFGT 141

Query: 134 DKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG 193
            + AFAKN  +E +RN +R+ F+ W Q+AFKN  V+P G GI HQ+NLE +   +  +  
Sbjct: 142 PQ-AFAKNVELEYQRNGERYRFLKWGQQAFKNFRVVPPGTGICHQVNLEYLGQTVWTKEE 200

Query: 194 ----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGK 249
               +A+PDT VGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M LP++IG +LTGK
Sbjct: 201 DGETIAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLLPEVIGFKLTGK 260

Query: 250 PQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMF 309
            + G+TATD+VL + + LR + VVS ++EFFG G + + L DRATI NM PE+GAT   F
Sbjct: 261 LKEGVTATDLVLTVVQMLRKKGVVSKFVEFFGPGMDNMPLADRATIGNMGPEYGATCGFF 320

Query: 310 YIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSD-DLKQAVYPRTLHFDLSSVVRTIAG 368
            +D +T++YLT++GR  +++ LVE Y+K  G+W + D    V+  TL  DL  VV ++AG
Sbjct: 321 PVDGETINYLTMSGRTHDRIALVEAYSKAQGMWREGDGSDLVFTDTLELDLGDVVPSMAG 380

Query: 369 PSNPHARVPTSELAARGISGEVE---NEPGLMPD-------------GAVIIAAITSCTN 412
           P  P  R+    +A+ G +G ++    +PG + +             G V IAAITSCTN
Sbjct: 381 PKRPEGRIALENIAS-GFAGSMDADYKKPGQLNNRYAVEGTDFDLGHGDVAIAAITSCTN 439

Query: 413 TSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIV 472
           TSNP  +IAAGLLARNA AKGL  KPWVKTSLAPGS+ V  YL ++ L  +L+ LGF +V
Sbjct: 440 TSNPSVLIAAGLLARNAVAKGLKTKPWVKTSLAPGSQVVGEYLAKSGLQADLDKLGFNLV 499

Query: 473 GFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVA 532
           GF CTTC G SG L   I + + D+ L  + VLSGNRNF+GRI P  +  +LASPPLVVA
Sbjct: 500 GFGCTTCIGNSGPLPAPISKTINDKGLIVSGVLSGNRNFEGRISPDVQANYLASPPLVVA 559

Query: 533 YAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDL 592
           YA+AGT++ D+ K+ +G D++G PV L +IWP+  E+   I   V  E +   Y  +F  
Sbjct: 560 YALAGTVQKDLTKEPIGEDQNGNPVYLRDIWPTSHEVQEFIQKYVTRELYESKYADVFKG 619

Query: 593 SVDYGDKVSP---LYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDH 646
            V++     P    Y W   STY++ PPY+ G      G   +KG R L + GD ITTDH
Sbjct: 620 DVNWQAVQVPPGQTYAWDDNSTYVQNPPYFVGMGKKGTGVADIKGARVLGLFGDKITTDH 679

Query: 647 LSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGK 706
           +SP+ +I   S AG YL    +   DFN Y T RG+H    R TFAN +++N M   +G 
Sbjct: 680 ISPAGSIKAASPAGAYLIGHDVAVADFNQYGTRRGNHEVMMRGTFANIRIRNHMLGPNG- 738

Query: 707 VKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEA 766
            K+G      P    T +++A   Y     PL+I AG +YG GSSRDWAAKG  L GV+A
Sbjct: 739 -KEGGYTIHYPSKEETSIYDAAMQYKTEGVPLVIFAGVEYGNGSSRDWAAKGTNLLGVKA 797

Query: 767 IVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAPRADLTVIIT 824
           ++A+ FERIHR+NLVGMGV+P  F+ G    + G+ G E+  + G   I PR      IT
Sbjct: 798 VIAQSFERIHRSNLVGMGVIPFVFEEGTTWQSLGLKGDELVTIEGLDKIKPRERKIAKIT 857

Query: 825 RKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQD 860
             +G   EVP+  R+DT +EV     GG+LQ   +D
Sbjct: 858 YGDGTVKEVPLLSRVDTLDEVIYLNNGGILQTVLRD 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: 1976
Number of extensions: 110
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 Apr 09 2024. 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 2024 update 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