GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Pseudarthrobacter sulfonivorans Ar51

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_058929097.1 AU252_RS00805 acyl-CoA dehydrogenase family protein

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



>NCBI__GCF_001484605.1:WP_058929097.1
          Length = 381

 Score = 95.1 bits (235), Expect = 3e-24
 Identities = 89/343 (25%), Positives = 153/343 (44%), Gaps = 30/343 (8%)

Query: 60  WPKEYGGTGWSSVQHYIFNEELQAAPAPQPLA--FGVSMVGPVIYTFGSEEQKKRFLPRI 117
           +P   GG G       +F + + +      LA  F  ++  P +   GSE+  +R++   
Sbjct: 58  FPDALGGGGTQLDLMTVFEQMIHSGVPTGVLASLFSHTIALPSLVKHGSEDLHRRYVIPT 117

Query: 118 ANVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDP 177
              +     G +EPG GSD+A+L+TKA + GD ++ING KT+ T    AD++    RT  
Sbjct: 118 LEGEMIGALGLTEPGGGSDVAALRTKAVRDGDHYVINGSKTFITSGVRADFVTVAARTGA 177

Query: 178 AAKKQEGISFILVDMKTKGITV-RPIQTIDG-GHEVNEVFFDDVEVPLENLVGQENKGWD 235
           +  K  GIS  +VD  T G TV R ++ +     +  E+ F DV VP  NL+GQEN G+ 
Sbjct: 178 SGNK--GISLFVVDADTPGFTVSRKLEKMGWLSSDTAELSFVDVRVPASNLIGQENGGFR 235

Query: 236 YAKFLLGNERTGIA--RVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELK 293
                L +ER  +A     +++  +    +      + G+P+      R K+A +    +
Sbjct: 236 QLMEQLQSERLTMAVECTAVARRCLDLTIEWVRNRHTFGEPLSSRQVVRHKIAEM---AR 292

Query: 294 ALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLM-EVIGPFAAPYDVHGD 352
             ++    V +   +   G                +  +TE+ M +    +A  Y  H  
Sbjct: 293 QTDVASNYVWSTATRWAAG----------------EDVSTEVAMAKNTAVYAVEYVAHEA 336

Query: 353 DDSNETMDW--TAQIAPGYFNNRKVSIYGGSNEIQRNIICKAV 393
              +  M +    ++   Y + R + I GG+NEI  ++I K +
Sbjct: 337 VQLHGGMGFMRECEVERHYRDIRVMGIGGGTNEIMNDVIAKRI 379


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: 347
Number of extensions: 15
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: 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 Apr 09 2024. 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