GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Sporolactobacillus vineae SL153

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate WP_010631287.1 RH97_RS05205 3-hydroxyacyl-CoA dehydrogenase family protein

Query= CharProtDB::CH_091789
         (282 letters)



>NCBI__GCF_000246965.1:WP_010631287.1
          Length = 312

 Score =  189 bits (481), Expect = 5e-53
 Identities = 110/285 (38%), Positives = 166/285 (58%), Gaps = 6/285 (2%)

Query: 2   KKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEAT 61
           K + VIG+G MGSGIAQ+FA  G+ V++ DIK EF+D+    I++NL+ LV  G + EA 
Sbjct: 3   KTISVIGSGVMGSGIAQSFAVGGYSVIVNDIKQEFLDKAKKNIHENLNLLVGSGDLTEAD 62

Query: 62  KVEILTRISGTVDLNMAA-DCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120
           +   L RI  T DL  AA + DL+IEA  E +D+K  ++ DL    KP+ +++SNTS+  
Sbjct: 63  RNAALGRIRFTTDLKEAAGEADLIIEAIPEVIDLKWNLYDDLATYKKPDAVVSSNTSTFP 122

Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEV- 179
           IT++ +      K I  HFFNPA ++ LVE+++   T      +VK   ++IGK PV + 
Sbjct: 123 ITKLTARESFDGKFIITHFFNPANLVPLVEIVKKKDTDLNLVQSVKNLLLSIGKTPVVLK 182

Query: 180 AEAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHP---MGPLELGDFIGLD 236
            E  GF+ NR+   ++ EA  ++ +G+A  +D+DKA+  G       +GP  + DF GLD
Sbjct: 183 KEINGFIANRLQTALMREAFSLVGQGVADADDVDKAITAGPGFRWAFVGPTRIADFGGLD 242

Query: 237 ICLAIMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDYS 281
               + D +  +   S+  P  L+ K V    LG K+G+G Y YS
Sbjct: 243 TWKRVFDNIAPDLDKSEGAPE-LINKLVSTHKLGTKTGEGLYKYS 286


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: 251
Number of extensions: 14
Number of successful extensions: 5
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: 312
Length adjustment: 26
Effective length of query: 256
Effective length of database: 286
Effective search space:    73216
Effective search space used:    73216
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.

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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