GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS29205
          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:

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