Aligments for a candidate for acnD in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for acnD in Pseudomonas putida KT2440

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate PP_2336 PP_2336 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Putida:PP_2336
          Length = 862

 Score = 1435 bits (3715), Expect = 0.0
 Identities = 723/861 (83%), Positives = 772/861 (89%), Gaps = 2/861 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT YRK LPGT LDYFD R A+EAI PGAY  LPYTSRVLAENLVRRC+P  L ASL Q
Sbjct: 1   MNTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA KGGDPAQVNPVVP QLIVDH
Sbjct: 61  LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120

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

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPV+H+  GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLP+I+GV
Sbjct: 181 SPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPEIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGK  P ITATD+VLALTEFLR QKVV +YLEF GEGA ALTLGDRATISNM PE+GA
Sbjct: 241 ELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMF IDQQT+DYL LTGRE +QVKLVETYAK  GLW+D L  AVY RTL FDLSSVVR
Sbjct: 301 TAAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
            +AGPSNPHARV TS+LAA+GI+G  E  PG MPDGAVIIAAITSCTNTSNPRNVIAAGL
Sbjct: 361 NMAGPSNPHARVATSDLAAKGIAGSWEEVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           +ARNAN  GLTRKPWVK+SLAPGSKAVQLYLEEA L  ELE LGFGIV FACTTCNGMSG
Sbjct: 421 IARNANKLGLTRKPWVKSSLAPGSKAVQLYLEEAGLEKELEQLGFGIVAFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           KDVLG+  DGK +RL +IWPSD EIDAV+ A+VKPEQFRKVY PMF +  D G KV+PLY
Sbjct: 541 KDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEEDRGPKVAPLY 599

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
           DWRP STYIRRPPYWEGALAGERTL+GMRPLAVL DNITTDHLSPSNAIM+DSAAGEYL 
Sbjct: 600 DWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 659

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMA-IVDGKVKQGSLARIEPEGIVTR 723
           KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM    DG VKQGSLARIEPEG VTR
Sbjct: 660 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRNDDGSVKQGSLARIEPEGKVTR 719

Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783
           MWEAIETYM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM
Sbjct: 720 MWEAIETYMQRKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 779

Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843
           GVLPLEFK G +R T G+DG+E +DV+G+  PRA LT+++TR NGE +EVPVTCRLDTAE
Sbjct: 780 GVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANGECLEVPVTCRLDTAE 839

Query: 844 EVSIYEAGGVLQRFAQDFLES 864
           EVSIYEAGGVLQRFAQDFLE+
Sbjct: 840 EVSIYEAGGVLQRFAQDFLEA 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: 2236
Number of extensions: 90
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: 862
Length adjustment: 42
Effective length of query: 825
Effective length of database: 820
Effective search space:   676500
Effective search space used:   676500
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, or view the source code.

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