Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N1B4

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Pf1N1B4_3821 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821
          Length = 864

 Score = 1435 bits (3714), Expect = 0.0
 Identities = 719/861 (83%), Positives = 774/861 (89%), Gaps = 1/861 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT++RKPLPG+ LDYFD R A++AI+PGAY  LPYTSRVLAENLVRRC+P  LT SLKQ
Sbjct: 1   MNTEFRKPLPGSHLDYFDVRAAVDAISPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
            IE K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPAQVNPVVPTQLIVDH
Sbjct: 61  FIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GGFD +AF KNRAIEDRRNEDRFHFINWT+KAFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI  R+GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS+MRLP+ +GV
Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGK QPGITATD+VLALTE+LR QKVV ++LEFFGEGA ALTLGDRATISNM PE+GA
Sbjct: 241 ELTGKLQPGITATDMVLALTEYLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMFYIDQQT+DYL LTGRE EQV+LVE+YAK  GLW+D LK A Y R L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVESYAKQTGLWADSLKGAQYERGLTFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
            +AGPSNPHARV  S+LAA+GISG+ ++ PG MPDGAVIIAAITSCTNTSNPRNVIAAGL
Sbjct: 361 NMAGPSNPHARVAVSDLAAKGISGQWDDVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           LARNAN  GLTRKPWVK+SLAPGSK V LYL+EA L  ELE LGFG+V FACTTCNGMSG
Sbjct: 421 LARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTSELEQLGFGVVAFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAK AFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKNAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           KDVLG+  DGK +RL +IWPSD EIDAV+ ASVKPEQFR+VY PMF +  D G KV+PLY
Sbjct: 541 KDVLGV-VDGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHEDTGPKVAPLY 599

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
           DWR  STYIRRPPYWEGALAG R LKGMRPLAVL DNITTDHLSPSNAIM+DSAAGEYL 
Sbjct: 600 DWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 659

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724
           KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM   +GKVKQGSLAR+EPEG V RM
Sbjct: 660 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEGQVMRM 719

Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784
           WEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI AEGFERIHRTNLVGMG
Sbjct: 720 WEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMG 779

Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844
           VLPLEF+ G +R T  IDG+E +DVIG   PRA LT++I RKNGERVEVPVTCRLDTAEE
Sbjct: 780 VLPLEFQPGTDRHTLAIDGSETYDVIGDRTPRATLTLVINRKNGERVEVPVTCRLDTAEE 839

Query: 845 VSIYEAGGVLQRFAQDFLESN 865
           VSIYEAGGVLQRFAQDFLE +
Sbjct: 840 VSIYEAGGVLQRFAQDFLEES 860


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: 2241
Number of extensions: 95
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: 864
Length adjustment: 42
Effective length of query: 825
Effective length of database: 822
Effective search space:   678150
Effective search space used:   678150
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 17 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

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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