GapMind for catabolism of small carbon sources

 

Alignments 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.

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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:

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:

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:

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:

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