GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimD in Azospirillum brasilense Sp245

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate AZOBR_RS29205 AZOBR_RS29205 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20676
         (396 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS29205 AZOBR_RS29205 acyl-CoA
           dehydrogenase
          Length = 381

 Score =  177 bits (450), Expect = 3e-49
 Identities = 124/356 (34%), Positives = 183/356 (51%), Gaps = 27/356 (7%)

Query: 45  EWYRILNKKGWAVTHWPKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVS-MVGPVIYT 103
           E+ R L ++GW    WPK+YGG   S+++ Y+  EEL AA AP    +      GP++  
Sbjct: 48  EFSRKLGQRGWIGMAWPKQYGGHERSALERYVVLEELLAAGAPVAAHWIADRQSGPLLLK 107

Query: 104 FGSEEQKKRFLPRIANVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLA 163
            G+EEQK+  LPRIA  + ++C G SEP SGSDLA+++T+A      W +NG K WTT A
Sbjct: 108 VGTEEQKRSILPRIAAGEFFFCIGMSEPDSGSDLAAVRTRAVPVEGGWRVNGTKLWTTYA 167

Query: 164 QHADWIFCLCRTDPAAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPL 223
            HA  +   CRT  A  +  G S  LVD+   GIT+RPI  + G    NEV F+DV +P 
Sbjct: 168 HHAHAMILYCRTGAADDRHGGTSQFLVDLTLPGITIRPIADLSGARHFNEVVFEDVLLPH 227

Query: 224 ENLVGQENKGWDYAKFLLGNERTGIAR-VGMSKERIRRIKQLAAQVESGGKPVIEDPKFR 282
             L+GQE  GW+     L  ER+G  R +      +  ++ L +Q+          P   
Sbjct: 228 SALIGQEGDGWNQVMSELAYERSGPERFMSTFVLFVELVRALGSQM---------TPDAA 278

Query: 283 DKLAAVEIELKALELTQLRVVADEGKHGKGKPNPA--SSVLKIKGSEIQQATTELLMEVI 340
             L  + + L  L     R VA   + G+   NPA  +SV+K  G+ ++Q   E+  +++
Sbjct: 279 GALGRLGVHLVVLRRLS-RSVAGMLQDGR---NPALQASVVKDLGALVEQEIPEIARQLM 334

Query: 341 GPFAAPYDVHGDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
              A   D+   D  +  + ++   AP +      S+ GG+ EI R II +  LGL
Sbjct: 335 ---AMEPDLRSHDALSAVLGYSILNAPAF------SLRGGTREILRGIIARG-LGL 380


Lambda     K      H
   0.317    0.135    0.411 

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: 355
Number of extensions: 17
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: 396
Length of database: 381
Length adjustment: 30
Effective length of query: 366
Effective length of database: 351
Effective search space:   128466
Effective search space used:   128466
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: 50 (23.9 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 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