GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_412 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_412
          Length = 408

 Score =  172 bits (435), Expect = 3e-47
 Identities = 133/401 (33%), Positives = 211/401 (52%), Gaps = 32/401 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60
           +  VIG+G MG GI    A AG  V   D + ++L+QA+  +  + +     G + +G  
Sbjct: 10  RAAVIGAGTMGRGIVMCLANAGVTVQWVDNNPQMLEQALATVADTYAHSVRQGRIDQGEA 69

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           +  +AR+    D   A++  D VIEAV E+LELK+ IFR  +    P A+LA+NTS+L I
Sbjct: 70  DARIARV-TAADGYVAIRDVDLVIEAVYENLELKQKIFRELDGLLKPEAILASNTSALDI 128

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
             IA+V + PQ+V+G+HFF+P  +M L+EIVRG  T+  V+     + + M K ++V  +
Sbjct: 129 DAIAAVTRRPQQVLGLHFFSPAHIMKLLEIVRGAQTAPAVLDAALALGQRMGKVSVVSGN 188

Query: 181 VPGFFVNRVL-LRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYS 239
             GF  NR+L   ++EA   L+E   A   +VD +A++  GF MG F + D  G+D+ + 
Sbjct: 189 CDGFIGNRMLNTYVLEARKMLLEG--AYPYQVD-AALQAFGFAMGPFRMFDVVGVDLQWR 245

Query: 240 VWKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGK-------FVRPTLPSTS 292
             + ++  G  A       +L  QG+ G KSG+G+Y Y  PG         V   +   S
Sbjct: 246 S-RQLSGIGQDAPEVQVDNRLCEQGRFGQKSGNGFYHY-EPGSRQAEHDPQVDALVLQVS 303

Query: 293 KKLG--RYLISP----------AVNEVSYLLREGIVGK-DDAEKGCVLGLGLPK---GIL 336
           ++LG  R  I P           VNE + +L+EGI G   D +   + G G P    G +
Sbjct: 304 EELGFQRREIGPEEILERCLLALVNEGAKILQEGIAGSAHDIDLVYLNGYGFPADKGGPM 363

Query: 337 SYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           ++AD+ G+  +   L ++    G DH++P  ++  +   GK
Sbjct: 364 AWADQQGLADIHRRLIDLETRQG-DHWNPARVIGELAAAGK 403



 Score = 33.1 bits (74), Expect = 2e-05
 Identities = 28/122 (22%), Positives = 55/122 (45%), Gaps = 13/122 (10%)

Query: 295 LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEM 354
           +G  +++  V E   +L EG           +   G   G     D +G+D+   +    
Sbjct: 193 IGNRMLNTYVLEARKMLLEGAYPYQ--VDAALQAFGFAMGPFRMFDVVGVDLQWRS---- 246

Query: 355 RQTSGMDHYSPDPLLLS-MVKEGKLGRKSGQGFHTY------AHEEAKYSTIVVRVEPPL 407
           RQ SG+   +P+  + + + ++G+ G+KSG GF+ Y      A  + +   +V++V   L
Sbjct: 247 RQLSGIGQDAPEVQVDNRLCEQGRFGQKSGNGFYHYEPGSRQAEHDPQVDALVLQVSEEL 306

Query: 408 AW 409
            +
Sbjct: 307 GF 308


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: 555
Number of extensions: 29
Number of successful extensions: 4
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: 408
Length adjustment: 35
Effective length of query: 616
Effective length of database: 373
Effective search space:   229768
Effective search space used:   229768
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