GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Magnetospirillum magneticum AMB-1

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate WP_011386256.1 AMB_RS19750 3-hydroxybutyryl-CoA dehydrogenase

Query= CharProtDB::CH_091789
         (282 letters)



>NCBI__GCF_000009985.1:WP_011386256.1
          Length = 292

 Score =  322 bits (824), Expect = 8e-93
 Identities = 167/281 (59%), Positives = 200/281 (71%)

Query: 1   MKKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEA 60
           + K+ VIGAG MG+GIAQ  AA GF+V+L D+ +E + +GL  I KNL + + KGK+ EA
Sbjct: 4   INKIGVIGAGQMGNGIAQVCAAAGFDVILLDVSEEALKKGLGTITKNLDRALSKGKLTEA 63

Query: 61  TKVEILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120
            K   L  I  T      +D DLVIEAA E   IK+ IFA L  + KPE  +ASNTSSLS
Sbjct: 64  EKAATLGHIKTTTAYADFSDSDLVIEAATEDEKIKRAIFAQLCPVLKPEAHIASNTSSLS 123

Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVA 180
           IT + +AT RP K +GMHF NP PVMKLVE+IRGIATS+ETF  V E +  +GK  V   
Sbjct: 124 ITRLGAATDRPAKFMGMHFMNPVPVMKLVELIRGIATSEETFSLVTEMTQKLGKKAVAAE 183

Query: 181 EAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLA 240
           + P F+VNRIL+PMINEAV  L EG+ SV  ID AMKLGANHPMGPLEL DFIGLD CLA
Sbjct: 184 DFPAFIVNRILLPMINEAVYTLYEGVGSVASIDTAMKLGANHPMGPLELADFIGLDTCLA 243

Query: 241 IMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDYS 281
           +M VL+    D+KYRP  LL KYV AGWLGRK+G+GFYDY+
Sbjct: 244 VMQVLHEGLADTKYRPCPLLVKYVEAGWLGRKTGRGFYDYT 284


Lambda     K      H
   0.319    0.137    0.386 

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: 268
Number of extensions: 4
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: 282
Length of database: 292
Length adjustment: 26
Effective length of query: 256
Effective length of database: 266
Effective search space:    68096
Effective search space used:    68096
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 (21.7 bits)
S2: 47 (22.7 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