GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas putida KT2440

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate PP_2047 PP_2047 3-hydroxyacyl-CoA dehydrogenase family protein

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Putida:PP_2047
          Length = 412

 Score =  169 bits (429), Expect = 2e-46
 Identities = 133/408 (32%), Positives = 207/408 (50%), Gaps = 32/408 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60
           +V VIG+G MG GI    A AG  V   D +   L+  +  +  + ++  +   + +   
Sbjct: 9   QVAVIGAGTMGRGIVISLANAGLSVLWLDCNAAALEAGLGMVSQAWAQQVDKQRITQAQA 68

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           +  LAR+    D   AL  +D VIEAV E+L LK+ IF   +AH  P A+LA+NTS+L I
Sbjct: 69  DACLARVQA-VDGYPALAEADLVIEAVYENLALKQEIFCALDAHLKPRAILASNTSALDI 127

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
             IA+V + P +V+G+HFF+P  +M L+EIVRG  T  +V+     + + M K  IV  +
Sbjct: 128 DAIAAVTQRPSQVLGLHFFSPAHVMKLLEIVRGTHTDQKVLDAAKALGERMGKVAIVAGN 187

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
            PGF  NR+L   +     L+ +G A   +VD + +++ GF MG F + D  G+D+ +  
Sbjct: 188 CPGFIGNRMLRSYVGEARKLLLEG-ALPHQVD-AVLQQFGFAMGPFRMYDVVGIDLEWRA 245

Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGK-------FVRPTLPSTSK 293
            + +  +G           L   G+LG K+G GYY+Y +PG         V   +   S+
Sbjct: 246 -RQLAGQGMHDPLVQVDNALCELGRLGQKTGQGYYRY-APGSRQAEHDPQVDALVLQVSQ 303

Query: 294 KLG-------------RYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---GIL 336
            LG             R L++  VNE + +L+EGI     D ++  + G G P    G +
Sbjct: 304 NLGYRRRGISAEEILERCLLA-LVNEGAKVLQEGIAASSGDIDQVWLHGYGFPAATGGPM 362

Query: 337 SYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGKLGRKSGQ 384
            +ADE G   ++  LE ++   G +H+ P  LL S+V  GK     G+
Sbjct: 363 RWADEQGAPFILARLEYLQGVLG-EHWRPAGLLYSLVAGGKRFEPRGE 409



 Score = 33.1 bits (74), Expect = 2e-05
 Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 11/99 (11%)

Query: 295 LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEM 354
           +G  ++   V E   LL EG +         +   G   G     D +GID+        
Sbjct: 192 IGNRMLRSYVGEARKLLLEGALPHQ--VDAVLQQFGFAMGPFRMYDVVGIDLEWRA---- 245

Query: 355 RQTSGMDHYSPDPLLL---SMVKEGKLGRKSGQGFHTYA 390
           RQ +G   +  DPL+    ++ + G+LG+K+GQG++ YA
Sbjct: 246 RQLAGQGMH--DPLVQVDNALCELGRLGQKTGQGYYRYA 282


Lambda     K      H
   0.316    0.134    0.377 

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: 559
Number of extensions: 36
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 651
Length of database: 412
Length adjustment: 35
Effective length of query: 616
Effective length of database: 377
Effective search space:   232232
Effective search space used:   232232
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 (21.6 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 (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