GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Methylibium petroleiphilum PM1

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>NCBI__GCF_000015725.1:WP_041929725.1
          Length = 391

 Score =  687 bits (1774), Expect = 0.0
 Identities = 333/388 (85%), Positives = 362/388 (93%)

Query: 5   ASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGL 64
           ASF+W DPLLLD QL+E+ER VRD+A  + +D+LAPRVLEAFRHE+TDPAIFREMGE+GL
Sbjct: 3   ASFHWDDPLLLDSQLSEDERAVRDAAQAYCRDRLAPRVLEAFRHEKTDPAIFREMGELGL 62

Query: 65  LGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKY 124
           LGAT+PE YGG+GLN+VCYGL+AREVER+DSGYRSMMSVQSSLVMVPI+ FGTEAQKQKY
Sbjct: 63  LGATLPEAYGGAGLNHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKY 122

Query: 125 LPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWA 184
           LPKLA GEWIGCFGLTEPNHGSDPGS+ TRAR V GGY L+G+KMWITNSPIADVFVVWA
Sbjct: 123 LPKLARGEWIGCFGLTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWA 182

Query: 185 KDDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKGP 244
           KDD G IRGF+L+KG +GL APA+HGKVGLRAS+TGEIVMD VF PEEN FP+VRGLKGP
Sbjct: 183 KDDGGQIRGFILDKGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAFPEVRGLKGP 242

Query: 245 FTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLA 304
           FTCLNSARYGI+WGALGAAE C+H ARQY LDR QFGRPLAANQLIQKKLADMQTEITL 
Sbjct: 243 FTCLNSARYGIAWGALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLG 302

Query: 305 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVN 364
           LQGCLRLGRMKDEGTAAVEITSIMKRNSCGK+L+IARMARDM+GGNGISDEFGVARHLVN
Sbjct: 303 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVN 362

Query: 365 LEVVNTYEGTHDVHALILGRAQTGIQAF 392
           LEVVNTYEGTHDVHALILGRA TGIQAF
Sbjct: 363 LEVVNTYEGTHDVHALILGRAITGIQAF 390


Lambda     K      H
   0.320    0.137    0.413 

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: 616
Number of extensions: 16
Number of successful extensions: 1
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: 393
Length of database: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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