GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pontibacter ramchanderi LP43

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate WP_101442918.1 BD749_RS03200 3-hydroxybutyryl-CoA dehydrogenase

Query= CharProtDB::CH_091789
         (282 letters)



>NCBI__GCF_002846395.1:WP_101442918.1
          Length = 301

 Score =  306 bits (784), Expect = 4e-88
 Identities = 155/282 (54%), Positives = 201/282 (71%), Gaps = 1/282 (0%)

Query: 1   MKKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEA 60
           MKK+ VIG+GTMG+GIA  FA  GF V L DI +E +++ L  I KNL +++ KG + E 
Sbjct: 1   MKKIAVIGSGTMGNGIAHVFAQNGFAVSLVDISEEALNKALATITKNLDRIIAKGNLTEE 60

Query: 61  TKVEILTRISGTVDLNMAA-DCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSL 119
            K + L RI+   ++     + DL++EAA E +D+K +IF DLD+  KPE ILASNTSS+
Sbjct: 61  QKSQTLGRITTYTNMQQGVQEADLIVEAATENVDLKLKIFKDLDSFAKPEAILASNTSSI 120

Query: 120 SITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEV 179
           SIT++AS T RPDKVIGMHF NP PVMKLVE+IRG +TS E    V + S+ +GK P E 
Sbjct: 121 SITKIASVTNRPDKVIGMHFMNPVPVMKLVEIIRGYSTSDEVTSQVMDMSLQLGKVPTEC 180

Query: 180 AEAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICL 239
            + PGFV NRIL+PMINEA+  L EG+A VE+ID  MKLG  HPMGPL+L DFIGLD+CL
Sbjct: 181 NDYPGFVANRILMPMINEAIYSLYEGVAGVEEIDTIMKLGMAHPMGPLQLADFIGLDVCL 240

Query: 240 AIMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDYS 281
           +I++VL+   G+ KY P  LL   V+AG  G KSG+GFY ++
Sbjct: 241 SILNVLHDGFGNPKYAPCPLLVNMVQAGHKGVKSGQGFYSWT 282


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: 266
Number of extensions: 9
Number of successful extensions: 2
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: 301
Length adjustment: 26
Effective length of query: 256
Effective length of database: 275
Effective search space:    70400
Effective search space used:    70400
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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