GapMind for catabolism of small carbon sources

 

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

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate 201903 SO2768 acyl-CoA dehydrogenase family protein (NCBI ptt file)

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__MR1:201903
          Length = 596

 Score = 88.2 bits (217), Expect = 6e-22
 Identities = 93/365 (25%), Positives = 154/365 (42%), Gaps = 49/365 (13%)

Query: 69  TIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPK 128
           T    +GG G+  V  G+   E++   +   +M    +      I+  GSE  KQKYLPK
Sbjct: 94  TCDPAFGGQGLPEVV-GIFVTEMQTSTNMAFAMYPGLTHGAYSAIHAHGSEALKQKYLPK 152

Query: 129 LATGEWVGCFGLTEPNHGSDPGSMVTRA-RKVDGGYSLSGAKMWITNS--PIAD--VFVV 183
           L +GEW G   LTE + G+D   + T+A    DG ++++G K++I++   P  D  V +V
Sbjct: 153 LVSGEWTGTMNLTESHAGTDLALLRTKAVPAADGYFAITGEKIFISSGDHPFTDNIVHLV 212

Query: 184 WAK--DDAGDIRGFVL---------EKGWKG----LSAPAIHGKVGLRASITGEIVMDEV 228
            A+  D    ++G  L           G  G    L A  +  K+G+  + T  +V D  
Sbjct: 213 LARLPDAPEGVKGISLFAVPKVLVNSDGSLGQANSLYASGLEHKMGIHGNSTCVMVFDGA 272

Query: 229 FCPEENAFPTVRGLKGPFTCLNSARYGIAWGALGAAEACYETARQYTMDRKQ-------- 280
               E      +GL+  FT +N AR G+    LG +E  Y+ A  Y  DR Q        
Sbjct: 273 L--GELVGEPHQGLRAMFTMMNQARLGVGMQGLGVSEIAYQNALAYAKDRLQSRAISGAK 330

Query: 281 --------------FGRPLAANQLIQKKLADMLTEITLGLQGCLR---LGRLKDEGNAPV 323
                           R L + +   +    ++ +  L L    R     + K       
Sbjct: 331 APEKAADPILVHGDVRRMLLSQKAFNEGARALVGQQALWLDEAERHSDPAKAKAASQLAA 390

Query: 324 ELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTHDIHAL-I 382
             T ++K     +  +    A+ + GG+G   E+ + + + +  +   YEGT+ I AL +
Sbjct: 391 LFTPVVKGFITNRGFNACVDAQQVFGGHGYIHEWGMEQFVRDSRIALIYEGTNGIQALDL 450

Query: 383 LGRAI 387
           +GR +
Sbjct: 451 VGRKL 455


Lambda     K      H
   0.319    0.136    0.409 

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: 520
Number of extensions: 24
Number of successful extensions: 2
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: 395
Length of database: 596
Length adjustment: 34
Effective length of query: 361
Effective length of database: 562
Effective search space:   202882
Effective search space used:   202882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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