Alignments for a candidate for acnD in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas benzenivorans DSM 8628

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_090439551.1 BLS63_RS00675 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_900100495.1:WP_090439551.1
          Length = 869

 Score = 1406 bits (3640), Expect = 0.0
 Identities = 694/866 (80%), Positives = 769/866 (88%), Gaps = 8/866 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MN+QYRKPL GT LDYFDTREA++AIAPGAYAKLPYTSRVLAE LVRRCEP+ LT SLKQ
Sbjct: 1   MNSQYRKPLAGTVLDYFDTREAVDAIAPGAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE K++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDP++VNPVVPTQLIVDH
Sbjct: 61  LIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120

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

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI AR GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLG  S MRLPDI+GV
Sbjct: 181 SPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           +LTGK QPGITATDIVLA+TEFLR ++VV +Y+EFFGEGA++L++GDRATISNM PE+GA
Sbjct: 241 KLTGKRQPGITATDIVLAITEFLRKERVVGAYVEFFGEGADSLSIGDRATISNMCPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TA+MFYIDQQT+DYL LTGRE EQV LVE YAK  GLW+D L  A Y R L FDLS+VVR
Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVENYAKLTGLWADALVTAEYERVLEFDLSTVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGI-------SGEVENEPGLMPDGAVIIAAITSCTNTSNPR 417
            +AGPSNPH R+PTS L  RGI       SG+VE   GL+PDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHKRLPTSALHERGIADEAKLASGKVEEAEGLLPDGAVIIAAITSCTNTSNPR 420

Query: 418 NVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACT 477
           NV+AAGLLA+ ANA GL RKPWVKTS APGSK  +LYLE+A LL ELE LGFGIVG+ACT
Sbjct: 421 NVVAAGLLAKKANALGLLRKPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACT 480

Query: 478 TCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 537
           TCNGMSGALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG
Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 540

Query: 538 TIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYG 597
           T+RFDIE+DVLG DK+G  + L ++WPSD EIDA++AASVKPEQF+++Y PMFDL     
Sbjct: 541 TVRFDIEQDVLGTDKNGNLITLKDLWPSDEEIDAIVAASVKPEQFKQIYIPMFDLGT-IQ 599

Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657
           +  SPLYDWRP STYIRRPPYWEGALAGERTLKGMRPLA+L DNITTDHLSPSNAI++DS
Sbjct: 600 EAESPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDS 659

Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717
           AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANP+L NEMA+VDG VK+GSLAR+EP
Sbjct: 660 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGVVKKGSLARVEP 719

Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777
           EG V RMWEAIETYM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHR
Sbjct: 720 EGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 779

Query: 778 TNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTC 837
           TNLVGMGVLP+EFK G  R T G+DG+E +D+ G ++PR +L ++I R+NGE  +VPVTC
Sbjct: 780 TNLVGMGVLPVEFKPGTTRLTLGLDGSETYDIEGDVSPRCELILVIHRRNGEVTQVPVTC 839

Query: 838 RLDTAEEVSIYEAGGVLQRFAQDFLE 863
           RLDTA EV +Y+AGGVLQRFAQDFLE
Sbjct: 840 RLDTAAEVHVYKAGGVLQRFAQDFLE 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: 2246
Number of extensions: 81
Number of successful extensions: 3
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.

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