GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Methylibium petroleiphilum PM1

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-17424
         (375 letters)



>NCBI__GCF_000015725.1:WP_041929725.1
          Length = 391

 Score =  206 bits (523), Expect = 1e-57
 Identities = 128/371 (34%), Positives = 193/371 (52%), Gaps = 5/371 (1%)

Query: 3   VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62
           ++++++ + DA +A+ ++RL P   +  +  +       EM ELGL G  +PE +GG+  
Sbjct: 17  LSEDERAVRDAAQAYCRDRLAPRVLEAFRHEKTDPAIFREMGELGLLGATLPEAYGGAGL 76

Query: 63  GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122
            +V Y +   E+   D    ++MSV +S+  VPI  FG E QK+++L  LA G  +G F 
Sbjct: 77  NHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKYLPKLARGEWIGCFG 136

Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182
           LTEP  GSD  SL TRAR     YVL+G+K +IT+   A V +V+A  D   G+  I  F
Sbjct: 137 LTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWAKDD--GGQ--IRGF 192

Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242
           I+     G +   V  K+G  AS T +IV D V  P  N    E  G K     L   R 
Sbjct: 193 ILDKGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAF-PEVRGLKGPFTCLNSARY 251

Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302
           GIA  A+G A   F  AR Y  +R  FG+PL  +Q +  +LADM T+I++  Q  L    
Sbjct: 252 GIAWGALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLGLQGCLRLGR 311

Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362
           ++D G  A+   S+ K  +   + ++   A   +GG G   +F + R   ++ V   YEG
Sbjct: 312 MKDEGTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVNLEVVNTYEG 371

Query: 363 TSDIQRMVIAR 373
           T D+  +++ R
Sbjct: 372 THDVHALILGR 382


Lambda     K      H
   0.319    0.134    0.382 

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: 354
Number of extensions: 15
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: 375
Length of database: 391
Length adjustment: 30
Effective length of query: 345
Effective length of database: 361
Effective search space:   124545
Effective search space used:   124545
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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