GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Shewanella oneidensis MR-1

Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate 201903 SO2768 acyl-CoA dehydrogenase family protein (NCBI ptt file)

Query= CharProtDB::CH_091785
         (379 letters)



>FitnessBrowser__MR1:201903
          Length = 596

 Score =  125 bits (314), Expect = 3e-33
 Identities = 101/325 (31%), Positives = 157/325 (48%), Gaps = 50/325 (15%)

Query: 96  SLINEHGTEEQKQKYLVPLAKGEKIGAYGLTEPNAGTDSGAQQTVAVLEGD-HYVINGSK 154
           S I+ HG+E  KQKYL  L  GE  G   LTE +AGTD    +T AV   D ++ I G K
Sbjct: 135 SAIHAHGSEALKQKYLPKLVSGEWTGTMNLTESHAGTDLALLRTKAVPAADGYFAITGEK 194

Query: 155 IFITNGGVADT-----FVIFAMTDRTKGTKGISAFIIEKGF--KGFSIGK--------VE 199
           IFI++G    T      V+  + D  +G KGIS F + K       S+G+        +E
Sbjct: 195 IFISSGDHPFTDNIVHLVLARLPDAPEGVKGISLFAVPKVLVNSDGSLGQANSLYASGLE 254

Query: 200 QKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLDGGRIGIAAQALGIAEGAFN 259
            K+GI  +ST  +VF+  +     ++G+  +G       ++  R+G+  Q LG++E A+ 
Sbjct: 255 HKMGIHGNSTCVMVFDGAL---GELVGEPHQGLRAMFTMMNQARLGVGMQGLGVSEIAYQ 311

Query: 260 EARAYMKERKQFGRSLDKFQG-------------LAWMMADMDVAIESARYLV-YKAAYL 305
            A AY K+R Q  R++   +              +  M+       E AR LV  +A +L
Sbjct: 312 NALAYAKDRLQ-SRAISGAKAPEKAADPILVHGDVRRMLLSQKAFNEGARALVGQQALWL 370

Query: 306 KQAGLPYTVDAARAKLHA--------------ANVAMDVTTKAVQLFGGYGYTKDYPVER 351
            +A      D A+AK  +               N   +    A Q+FGG+GY  ++ +E+
Sbjct: 371 DEA--ERHSDPAKAKAASQLAALFTPVVKGFITNRGFNACVDAQQVFGGHGYIHEWGMEQ 428

Query: 352 MMRDAKITEIYEGTSEVQKLVISGK 376
            +RD++I  IYEGT+ +Q L + G+
Sbjct: 429 FVRDSRIALIYEGTNGIQALDLVGR 453


Lambda     K      H
   0.317    0.135    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: 488
Number of extensions: 28
Number of successful extensions: 6
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: 379
Length of database: 596
Length adjustment: 33
Effective length of query: 346
Effective length of database: 563
Effective search space:   194798
Effective search space used:   194798
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 (21.7 bits)
S2: 51 (24.3 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