Alignments for a candidate for acnD in Novosphingobium fuchskuhlense FNE08-7

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Novosphingobium fuchskuhlense FNE08-7

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_067906659.1 AQZ52_RS04200 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001519075.1:WP_067906659.1
          Length = 889

 Score =  682 bits (1759), Expect = 0.0
 Identities = 377/859 (43%), Positives = 523/859 (60%), Gaps = 42/859 (4%)

Query: 29  AIAPGAYAKLPYTSRVLAENLVRRCEP--EMLTASLKQIIESKQE----LDFPWFPARVV 82
           A A G  ++LP++ +VL ENL+R  +    + T  +K +++ +++     +  + PARV+
Sbjct: 31  AAAYGDVSRLPFSMKVLLENLLRFEDGGFTVSTDDIKALVDWQKDPSSSREIQYRPARVL 90

Query: 83  CHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNR 142
             D  G   +VDLA +RDAIA  GGD +++NP+VP  L++DHS+ V+  G  K AF +N 
Sbjct: 91  LQDFTGVPCVVDLAAMRDAIAKLGGDTSRINPLVPVHLVIDHSVMVDEFGHPK-AFEQNV 149

Query: 143 AIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG-----VAFP 197
            IE  RN +R+ F+ W  K+  N   +P G GI HQ+NLE ++  +    G     VA+P
Sbjct: 150 EIEYYRNGERYDFLKWGSKSLANFKAVPPGTGICHQVNLEHIAQAVWTSEGPDGTTVAYP 209

Query: 198 DTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITAT 257
           DT VGTDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P+++G + TG+ + G+TAT
Sbjct: 210 DTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVVGFKFTGELKEGVTAT 269

Query: 258 DIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLD 317
           D+VL  T  LR   VV  ++E++G G  +LTL DRAT++NM PE+GAT   F ID +TLD
Sbjct: 270 DLVLTCTSMLRKHGVVGRFVEYYGPGLASLTLADRATLANMAPEYGATCGFFGIDDKTLD 329

Query: 318 YLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVP 377
           Y+ LTGR+  Q+ L E YAK  G W D   + V+  TL  DL +VV ++AGP  P  RV 
Sbjct: 330 YMRLTGRDENQIALTEAYAKAQGFWIDPSIEPVFTSTLELDLGTVVPSLAGPKRPQDRVS 389

Query: 378 --------------TSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAG 423
                         T + A + +   VE     + DG V IAAITSCTNTSNP  ++AAG
Sbjct: 390 LPDVDDVFNADMANTYKKAQQRV--PVEGMDFDIGDGDVTIAAITSCTNTSNPGVLVAAG 447

Query: 424 LLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMS 483
           L+A+ AN  GL  KPWVKTSLAPGS+ V  YL  A L   L+++GF +VG+ CTTC G S
Sbjct: 448 LVAKKANELGLKPKPWVKTSLAPGSQVVTDYLVRAGLQEHLDAVGFNLVGYGCTTCIGNS 507

Query: 484 GALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDI 543
           G L   I + + +  L A AV+SGNRNF+GR+ P  +  FLASPPLVVAYA+ GT+  D 
Sbjct: 508 GPLAEPISKAINENGLVAAAVISGNRNFEGRVSPDVRANFLASPPLVVAYALKGTVIEDF 567

Query: 544 EKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDY---GDKV 600
               +G  KDG  V L +IWPS+ E+   +A  +    F+  Y  ++     +       
Sbjct: 568 VSTPIGQSKDGVDVYLKDIWPSNHEVYETMAGCMDRAMFQARYADVYKGDAHWQAINVAG 627

Query: 601 SPLYDWRPQSTYIRRPPYWEGAL---AGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657
           S  Y WR  STY+  PPY+EG     A    +   +PLA+LGD+ITTDH+SP+ +I  DS
Sbjct: 628 SETYSWRAGSTYVANPPYFEGMTMTPAPVGDIIEAKPLAILGDSITTDHISPAGSIKADS 687

Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717
            AG++L +  + + DFNSY   RG H    R TFAN ++KNEM  V G   +G ++R   
Sbjct: 688 PAGKWLMEHQVAKADFNSYGARRGHHEVMMRGTFANIRIKNEM--VPG--IEGGMSRYGA 743

Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777
           E  V  +++    +     PL++IAG +YG GSSRDWAAKG  L GV A++ E FERIHR
Sbjct: 744 E--VGAIYDVAMQHKADGTPLVVIAGKEYGTGSSRDWAAKGTNLLGVRAVIVESFERIHR 801

Query: 778 TNLVGMGVLPLEFKAGENRATYGIDGTEVFDV--IGSIAPRADLTVIITRKNGERVEVPV 835
           +NLVGMGVLPL+FK GE+R T G+ G + F +  +  + PR D+ V +TR +G       
Sbjct: 802 SNLVGMGVLPLQFKDGESRQTLGLTGDDTFTIRGVAGLKPRQDVEVEVTRADGSTFTFTA 861

Query: 836 TCRLDTAEEVSIYEAGGVL 854
            CR+DTA E+  Y  GG+L
Sbjct: 862 LCRIDTANELEYYLNGGIL 880


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: 100
Number of successful extensions: 9
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: 889
Length adjustment: 43
Effective length of query: 824
Effective length of database: 846
Effective search space:   697104
Effective search space used:   697104
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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