Alignments for a candidate for acnD in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Stenotrophomonas chelatiphaga DSM 21508

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_057508738.1 ABB28_RS11325 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001431535.1:WP_057508738.1
          Length = 871

 Score = 1440 bits (3727), Expect = 0.0
 Identities = 719/868 (82%), Positives = 775/868 (89%), Gaps = 7/868 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MN  YRK LPGTALDYFDTR A++AI PGAYA LPYTSRVLAENLVRRC+P  L ASL+Q
Sbjct: 1   MNESYRKNLPGTALDYFDTRAAVDAIQPGAYATLPYTSRVLAENLVRRCDPATLQASLRQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE +Q+LDFPWFPARVVCHDILGQTALVDLAGLRDAIA  GGDPAQ+NPVVPTQLIVDH
Sbjct: 61  LIERRQDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADAGGDPAQINPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVEY GFDK AF +NRA+EDRRNEDRFHFINWT+KAFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVEYPGFDKAAFERNRAVEDRRNEDRFHFINWTRKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPV+  R+GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS+MRLPDIIGV
Sbjct: 181 SPVVQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPDIIGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTG+PQPGIT TDIVLALTEFLRA KVV +++EFFG GA AL++GDRATISNMTPEFGA
Sbjct: 241 ELTGRPQPGITCTDIVLALTEFLRAAKVVGAWIEFFGAGASALSIGDRATISNMTPEFGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMF IDQQTLDYL LTGRE  QV+LVETYAK AGLW+DDL Q  Y R L FDLSSVVR
Sbjct: 301 TAAMFSIDQQTLDYLRLTGREEPQVQLVETYAKAAGLWADDLAQVQYERVLQFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGI-------SGEVENEPGLMPDGAVIIAAITSCTNTSNPR 417
            +AGPSNPH RV TSELAARGI       SG++E   GLMPDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHKRVATSELAARGIADEAKLASGKLEQAGGLMPDGAVIIAAITSCTNTSNPR 420

Query: 418 NVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACT 477
           NVI A LLARNAN  GLTRKPWVK+SLAPGSKAVQLYLEEA LL ELE LGFGIVGFACT
Sbjct: 421 NVIGAALLARNANRAGLTRKPWVKSSLAPGSKAVQLYLEEAGLLGELEQLGFGIVGFACT 480

Query: 478 TCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 537
           TCNGMSGALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASP LVVAYAIAG
Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPALVVAYAIAG 540

Query: 538 TIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYG 597
           T+RFDIEKD LG+D  G  + L ++WPSD EIDAV+ ASVKPEQFRKVY+PMF  +V++G
Sbjct: 541 TVRFDIEKDALGVDAQGNSITLKDLWPSDEEIDAVVKASVKPEQFRKVYDPMFTFTVEHG 600

Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657
             +SPLY WRPQSTYIRRPPYWEGALAG RTL GMRPLAVLGDNITTDHLSPSNAI+  S
Sbjct: 601 APISPLYAWRPQSTYIRRPPYWEGALAGARTLSGMRPLAVLGDNITTDHLSPSNAILASS 660

Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717
           AAGEYL +MGLPEEDFNSYATHRGDHLTAQRATFANPKL NEMA+VDG VKQGSLAR+EP
Sbjct: 661 AAGEYLAQMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGVVKQGSLARVEP 720

Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777
           EG V RMWEAIETYM R+QPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI AEGFERIHR
Sbjct: 721 EGQVLRMWEAIETYMLRRQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHR 780

Query: 778 TNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTC 837
           TNL+GMGVLPLEFK G  R T GIDGTE FDV G+  PRA+LT++I R++G ++ VPVTC
Sbjct: 781 TNLIGMGVLPLEFKPGVTRLTLGIDGTETFDVTGARLPRAELTLVIHRRDGSQLMVPVTC 840

Query: 838 RLDTAEEVSIYEAGGVLQRFAQDFLESN 865
           RLDTAEEVSIYEAGGVLQRFAQDFLE++
Sbjct: 841 RLDTAEEVSIYEAGGVLQRFAQDFLEAS 868


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: 2211
Number of extensions: 84
Number of successful extensions: 2
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: 871
Length adjustment: 42
Effective length of query: 825
Effective length of database: 829
Effective search space:   683925
Effective search space used:   683925
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 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