Alignments for a candidate for acnD in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Thiothrix lacustris DSM 21227

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_028487612.1 Q394_RS0100860 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000621325.1:WP_028487612.1
          Length = 867

 Score = 1440 bits (3728), Expect = 0.0
 Identities = 717/866 (82%), Positives = 772/866 (89%), Gaps = 6/866 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT+YRK LPGT LDYFDTR AIEAI PG+YA LPYTSRVLAE LVRRCEPEMLT SLKQ
Sbjct: 1   MNTEYRKNLPGTKLDYFDTRAAIEAIQPGSYATLPYTSRVLAEQLVRRCEPEMLTDSLKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE KQ+LDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GG+PA+VNPVVPTQLIVDH
Sbjct: 61  LIEGKQDLDFPWYPARVVCHDILGQTALVDLAGLRDAIADQGGNPAKVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GGFD DAFAKNRAIEDRRNEDRFHFI WT+ AFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI AR+GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLG  S MRLPDIIGV
Sbjct: 181 SPVIQARDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIIGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           +L GK QPGITATDIVLA+TEFLR ++VVS++LEFFGEGA+ LT+GDRATISNMTPEFGA
Sbjct: 241 KLVGKRQPGITATDIVLAITEFLRKERVVSAWLEFFGEGAKNLTIGDRATISNMTPEFGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           +A MFYID+QT+DYL LTGRE EQV LVE YAK  GLW+D L  A YPR L FDLSSVVR
Sbjct: 301 SAGMFYIDEQTIDYLKLTGREPEQVALVENYAKATGLWADSLVDATYPRVLEFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGI-----SGEVENEPGLMPDGAVIIAAITSCTNTSNPRNV 419
            +AGPSNPH R+PT++LA RGI     + + E   G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHRRLPTADLAERGIAVNLAAAQAEEAEGKMPDGAVIIAAITSCTNTSNPRNV 420

Query: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479
           +AA LLARNAN  GL RKPWVKTS APGSK  +LYL+EA LL ELE LGFGIVGFACTTC
Sbjct: 421 VAAALLARNANKLGLVRKPWVKTSFAPGSKVAELYLQEAGLLTELEQLGFGIVGFACTTC 480

Query: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539
           NGMSGALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 481 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540

Query: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599
           RFDIEKDVLG DKDG P+ L +IWP+D EIDA++A SVKPEQF+++Y PMFDL     + 
Sbjct: 541 RFDIEKDVLGTDKDGNPITLKDIWPTDEEIDAIVATSVKPEQFKQIYIPMFDLGT-VEEA 599

Query: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659
            SPLYDWRP STYIRRPPYWEGALAGERTLKGM PLAVL DNITTDHLSPSNAIMM+SAA
Sbjct: 600 KSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMLPLAVLPDNITTDHLSPSNAIMMNSAA 659

Query: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEG 719
           GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEMA+VDGKVKQGSLAR+EPEG
Sbjct: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGKVKQGSLARVEPEG 719

Query: 720 IVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
            V RMWEAIETYM+RKQPLII+AGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN
Sbjct: 720 QVMRMWEAIETYMERKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779

Query: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRL 839
           LVGMGVLPLEFKAGE R TY IDGTE +DV G IAPR DLTVI+ R+NGE V +PVTCRL
Sbjct: 780 LVGMGVLPLEFKAGETRKTYAIDGTESYDVEGDIAPRTDLTVIMHRRNGETVRIPVTCRL 839

Query: 840 DTAEEVSIYEAGGVLQRFAQDFLESN 865
           DTA EV +Y AGGVLQRFAQDFLE +
Sbjct: 840 DTAAEVRVYNAGGVLQRFAQDFLEGD 865


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: 2225
Number of extensions: 103
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: 867
Length adjustment: 42
Effective length of query: 825
Effective length of database: 825
Effective search space:   680625
Effective search space used:   680625
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