GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Bacillus altitudinis 41KF2b

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase

Query= BRENDA::F4JML5
         (301 letters)



>NCBI__GCF_000691145.1:WP_035704417.1
          Length = 260

 Score =  223 bits (568), Expect = 4e-63
 Identities = 121/256 (47%), Positives = 161/256 (62%)

Query: 45  LNRLSGSDSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFC 104
           L   S  D  I  + L+RP   NA++  ML+ +    + I  D + R +++      VFC
Sbjct: 4   LVHFSIQDDYIGIMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFC 63

Query: 105 AGADLKERRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRI 164
           AGADLKERR M+  E    V +++  F+ IE+L +P IA I G ALGGGLE+ALACDLRI
Sbjct: 64  AGADLKERRLMTEQEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRI 123

Query: 165 CGENAVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICV 224
               A  GLPETGLAI+PGAGGTQRL RL+G   +KE+IFTG  + A EA   GL+    
Sbjct: 124 ARAGAALGLPETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERIS 183

Query: 225 TAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRL 284
           TA      AI +A+QI + GP+A+K AK+AI   ++ ++ +GL  E   Y +L++T+DRL
Sbjct: 184 TADSLMNDAITLAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRL 243

Query: 285 EGLAAFAEKRKPLYTG 300
           EGL AF EKR P Y G
Sbjct: 244 EGLKAFQEKRTPHYRG 259


Lambda     K      H
   0.318    0.134    0.373 

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: 148
Number of extensions: 5
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: 301
Length of database: 260
Length adjustment: 26
Effective length of query: 275
Effective length of database: 234
Effective search space:    64350
Effective search space used:    64350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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