Alignments for a candidate for acnD in Lysobacter daejeonensis GH1-9

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Lysobacter daejeonensis GH1-9

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_036138977.1 N800_RS12170 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000768355.1:WP_036138977.1
          Length = 869

 Score = 1427 bits (3694), Expect = 0.0
 Identities = 711/867 (82%), Positives = 781/867 (90%), Gaps = 7/867 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MN  +RKPLPGT LD+FD REA+EA+ PGA+A LPYT+RV AEN+VR+ +P M  A L+Q
Sbjct: 1   MNNAHRKPLPGTKLDWFDAREAVEALQPGAWATLPYTARVHAENIVRKADPAMRDAYLRQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           ++E +++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA KGGDPAQVNPVVP QLIVDH
Sbjct: 61  LVERRRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GGFD DAFAKNRAIEDRRNEDRFHFI+WT++AF+N+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFRNVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI+ ++GVAFPDT VGTDSHTPHVDALGVIA+GVGGLEAE+VMLGRAS+MRLPDI+GV
Sbjct: 181 SPVIYVQDGVAFPDTCVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGKPQPGITATDIVL+LTEFLR QKVV +YLEF GEGA ALT+GDRATISNM PE+GA
Sbjct: 241 ELTGKPQPGITATDIVLSLTEFLRKQKVVGAYLEFRGEGAAALTIGDRATISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMF+ID  TLDYL LTGR  EQV LVETYAK AGLW+DDL+ A Y RTLHFDLSSV R
Sbjct: 301 TAAMFFIDDNTLDYLRLTGRSDEQVALVETYAKAAGLWADDLRTAQYERTLHFDLSSVER 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVE-----NEPGLMPDGAVIIAAITSCTNTSNPRNV 419
           T+AGPSNPHAR+P ++LA RGI+G +E        GL+PDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TMAGPSNPHARLPVAQLAERGIAGNLEAARAQEAQGLLPDGAVIIAAITSCTNTSNPRNV 420

Query: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479
           IAAGLLARNA   GL RKPWVKTSLAPGSKAV LYL+EA L  +LE LGFGIV FACTTC
Sbjct: 421 IAAGLLARNAARLGLQRKPWVKTSLAPGSKAVALYLDEAGLTDDLEQLGFGIVAFACTTC 480

Query: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539
           NGMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540

Query: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599
           RFDIEKDVLG+  DG+ +RL ++WP+DAEIDAV+ A+VKPEQFRKVYEPMF++ V++G  
Sbjct: 541 RFDIEKDVLGV-VDGREIRLKDLWPTDAEIDAVMKAAVKPEQFRKVYEPMFNVRVEHGGA 599

Query: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659
           VSPLYDWRPQSTYIRRPPYWEGALAGERTL+GMRPLAVLGDNITTDHLSPSNAI++DSAA
Sbjct: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLRGMRPLAVLGDNITTDHLSPSNAILLDSAA 659

Query: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIV-DGKVKQGSLARIEPE 718
           GEYL KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM    DG V+QGSLARIEPE
Sbjct: 660 GEYLDKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRKDDGSVRQGSLARIEPE 719

Query: 719 GIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 778
           G VTRMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT
Sbjct: 720 GQVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 779

Query: 779 NLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCR 838
           NL+GMGVLPLEF+ G +R T  IDGTE +DVIG   PRA LT++I R+NGERVEVPVTCR
Sbjct: 780 NLIGMGVLPLEFQPGADRTTLAIDGTETYDVIGERTPRATLTLVIHRRNGERVEVPVTCR 839

Query: 839 LDTAEEVSIYEAGGVLQRFAQDFLESN 865
           LDTAEEVSIYEAGGVLQRFA DFLES+
Sbjct: 840 LDTAEEVSIYEAGGVLQRFANDFLESS 866


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: 2271
Number of extensions: 97
Number of successful extensions: 4
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: 869
Length adjustment: 42
Effective length of query: 825
Effective length of database: 827
Effective search space:   682275
Effective search space used:   682275
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