GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Streptacidiphilus oryzae TH49

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate WP_037568644.1 BS73_RS01520 alpha-ketoacid dehydrogenase subunit beta

Query= metacyc::MONOMER-11684
         (327 letters)



>NCBI__GCF_000744815.1:WP_037568644.1
          Length = 329

 Score =  249 bits (636), Expect = 7e-71
 Identities = 135/321 (42%), Positives = 202/321 (62%), Gaps = 4/321 (1%)

Query: 5   SYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIA 64
           +Y +A+  AM+E +  D RVF++GEDVGR GG F  + GL E+FG ER+ DTPL+ESA  
Sbjct: 6   TYREAMREAMREALRADERVFLMGEDVGRYGGCFGVSLGLLEEFGPERIRDTPLSESAFV 65

Query: 65  GVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVH 124
           G GIGAA+ G+RPI E+   +F + A++QI++ AA +++ S      P+V+R   G G  
Sbjct: 66  GAGIGAAINGLRPIVEIMTVNFSLLALDQILNNAATLQHMSGGQIQVPLVIRMTTGAGRQ 125

Query: 125 GALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYR---LIK 181
            A  HS S+E  +A+ PGL+++ P+T  DA+ +L AA+ D DPV+ FEH   Y     + 
Sbjct: 126 LAAQHSHSLEGWYAHIPGLRVLAPATLPDARHMLAAALADPDPVIVFEHGSLYNTAGALD 185

Query: 182 GEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYP 241
              PAD     I  A V+R G D++++ YG  +  AL+AAERL  DGISA V+DLRT+ P
Sbjct: 186 PGSPADSAAADITHAAVRRPGTDVSLVAYGGSLPKALEAAERLAADGISAEVLDLRTLRP 245

Query: 242 LDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMP 301
           LD+ A+     +T +V++V E  +   + +EVAA I+E   ++LDAPI+R+   ++P +P
Sbjct: 246 LDQPALTATVGRTHRVVVVDEGWRSVGLSAEVAARIAESAFYELDAPIERVCTAEVP-IP 304

Query: 302 YAPTMEKYFMVNPDKVEAAMR 322
           YA  +E+  +     + AA R
Sbjct: 305 YARGLEEAALPQAADIVAAAR 325


Lambda     K      H
   0.319    0.136    0.392 

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: 284
Number of extensions: 17
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: 327
Length of database: 329
Length adjustment: 28
Effective length of query: 299
Effective length of database: 301
Effective search space:    89999
Effective search space used:    89999
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: 49 (23.5 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