GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimF in Pseudomonas putida KT2440

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate PP_2047 PP_2047 3-hydroxyacyl-CoA dehydrogenase family protein

Query= metacyc::MONOMER-20678
         (699 letters)



>lcl|FitnessBrowser__Putida:PP_2047 PP_2047 3-hydroxyacyl-CoA
           dehydrogenase family protein
          Length = 412

 Score =  364 bits (934), Expect = e-105
 Identities = 192/402 (47%), Positives = 259/402 (64%), Gaps = 6/402 (1%)

Query: 292 PRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGL 351
           P P+++VA+IGAGTMG GI +S ANAG+ V  ++     L+ GLG++ + W     +  +
Sbjct: 4   PFPINQVAVIGAGTMGRGIVISLANAGLSVLWLDCNAAALEAGLGMVSQAWAQQVDKQRI 63

Query: 352 PPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTS 411
                   +A +  + G   + +ADL+IEAV+E +A+K+E+F A+DAH KP A+LASNTS
Sbjct: 64  TQAQADACLARVQAVDGYPALAEADLVIEAVYENLALKQEIFCALDAHLKPRAILASNTS 123

Query: 412 YLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPV 471
            L ID IAA T+RP  VLG+HFFSPA+VMKL EIVRG  T    L  A ++ +++ KV +
Sbjct: 124 ALDIDAIAAVTQRPSQVLGLHFFSPAHVMKLLEIVRGTHTDQKVLDAAKALGERMGKVAI 183

Query: 472 VVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGW 531
           V G C GF+GNRML +   ++ KLL EGALP QVDAV+ +FG  MGPF M D+ G+D+ W
Sbjct: 184 VAGNCPGFIGNRMLRSYVGEARKLLLEGALPHQVDAVLQQFGFAMGPFRMYDVVGIDLEW 243

Query: 532 RSRKDRGIKS-----EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLA 586
           R+R+  G        ++ +ALCE GR GQKTG+GYY+Y  GSR    DP+V+ L+     
Sbjct: 244 RARQLAGQGMHDPLVQVDNALCELGRLGQKTGQGYYRYAPGSRQAEHDPQVDALVLQVSQ 303

Query: 587 KLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMH 646
            LG +RR I+ EEILER +  ++NEGA++L+E IAA   DID VWL+GYG+P   GGPM 
Sbjct: 304 NLGYRRRGISAEEILERCLLALVNEGAKVLQEGIAASSGDIDQVWLHGYGFPAATGGPMR 363

Query: 647 YADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           +AD  G   I  RL  Y +        PA LL  L A GK F
Sbjct: 364 WADEQGAPFILARLE-YLQGVLGEHWRPAGLLYSLVAGGKRF 404


Lambda     K      H
   0.317    0.134    0.383 

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: 637
Number of extensions: 34
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: 699
Length of database: 412
Length adjustment: 35
Effective length of query: 664
Effective length of database: 377
Effective search space:   250328
Effective search space used:   250328
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: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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