Alignments for a candidate for acnD in Lactobacillus silagei IWT126

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Lactobacillus silagei IWT126

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_089136258.1 CES79_RS02945 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_002217945.1:WP_089136258.1
          Length = 874

 Score =  687 bits (1772), Expect = 0.0
 Identities = 368/837 (43%), Positives = 513/837 (61%), Gaps = 29/837 (3%)

Query: 37  KLPYTSRVLAENLVRRCEPEMLTASLKQII---ESKQELDFPWFPARVVCHDILGQTALV 93
           KLPYT R+L E  +RR + +     +       +   + +    P RV+  D+ G  ALV
Sbjct: 34  KLPYTIRILLEEALRRADQKPDQGRVPSAFNDWDQHHDQNIAHQPERVILQDLTGVPALV 93

Query: 94  DLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRF 153
           DLA +RD +A +GGD   +NP +P  L++DHS+ V++ G +K AFA N   E +RN +R+
Sbjct: 94  DLAAMRDVVAKRGGDVNSINPEIPVHLVIDHSVQVDHAG-NKQAFAYNIQQEFKRNRERY 152

Query: 154 HFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGV-----AFPDTLVGTDSHTP 208
            F+ W Q +FKN+ VIP   GI+HQ+NLE ++ VIH +        AFPDTLVGTDSHT 
Sbjct: 153 TFLKWAQNSFKNLTVIPPDTGIIHQVNLEYLADVIHPKQLADGSYEAFPDTLVGTDSHTT 212

Query: 209 HVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLR 268
            ++ LGV+  GVGG+EAES MLG  +YM +P ++GV+LTG+   GITATD+ L LT  LR
Sbjct: 213 MINGLGVLGWGVGGIEAESSMLGEPTYMPMPKVVGVKLTGRLGEGITATDLALTLTHLLR 272

Query: 269 AQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQ 328
              VV  ++EF+GEGA++L L  RATI NM PE+GAT   F IDQQT+DYL LT R A+Q
Sbjct: 273 EHNVVGKFVEFYGEGAQSLPLAYRATIGNMAPEYGATCGFFPIDQQTIDYLKLTNRSADQ 332

Query: 329 VKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAAR---- 384
           + LVE YAKT  L+ D+     Y  T+  DL+SV  ++AGP+ P   V   ++  +    
Sbjct: 333 IDLVENYAKTNSLFYDEKAIPQYSETVSLDLASVQSSLAGPNRPQDTVALKDMPKQFDDR 392

Query: 385 ----GISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWV 440
                    V  +   +  G++ IAAITSCTNTSNP+ ++AAGL+A+ A   GL    +V
Sbjct: 393 RQLPDYPVTVNGQKFKIRVGSIGIAAITSCTNTSNPKVLLAAGLVAKRAVELGLKVPDYV 452

Query: 441 KTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLY 500
           KTSLAPGS+ V  YLE A L P L+ LGF +VG+ C TC G SG L   +Q  + +    
Sbjct: 453 KTSLAPGSRVVTQYLEAAGLQPYLDQLGFNLVGYGCMTCIGNSGQLKEDLQTRLTEHPYP 512

Query: 501 ATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLI 560
             AV S NRNF GR++P  K  +LASPPLVV YA+AGT   D+    +G  K G PV L 
Sbjct: 513 IAAVESANRNFAGRVNPLVKDTYLASPPLVVIYALAGTCDIDLTTQPVGTSKSGTPVYLK 572

Query: 561 NIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPP 617
           ++WP D+E+  +    +KP++F+K Y+ +   ++ + +  +P    Y W  +STYI  PP
Sbjct: 573 DLWPKDSEVAQLEQQYLKPKEFQKNYQSILSQNMTWDELPAPQSATYQWDVRSTYIAAPP 632

Query: 618 YWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYA 677
           +++GA AG + L G+R LA LGD+ITTDH+SP+  I  ++ AG YL   G+  +DFNSY 
Sbjct: 633 FFDGA-AGSKQLSGLRVLAKLGDSITTDHISPAGFIGAETPAGRYLKSKGIATKDFNSYG 691

Query: 678 THRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQP 737
           + RG+H    R T AN +LKN++       K G   R  P    T ++EA + Y      
Sbjct: 692 SRRGNHEVMMRGTLANIRLKNQLT----PDKTGGFTRYLPTNKETTIFEAAQQYQTDHTG 747

Query: 738 LIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRA 797
           L+++AG DYG GSSRDWAAKGV+L GV+AI+AE FERIHR NL  MGV+PL+++ G+   
Sbjct: 748 LVVLAGKDYGMGSSRDWAAKGVKLLGVKAIIAESFERIHRANLAMMGVVPLQYQPGQTAE 807

Query: 798 TYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           + G+DGTE F    SI     +  ++ +K  ++ +     R DT  +   Y  GG++
Sbjct: 808 SLGLDGTETF----SIELDGQVAHVMAQKADQQTKFDAIVRFDTPVDWKYYRNGGIM 860


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: 1816
Number of extensions: 79
Number of successful extensions: 8
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: 874
Length adjustment: 42
Effective length of query: 825
Effective length of database: 832
Effective search space:   686400
Effective search space used:   686400
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 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