GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Rhizobium etli CFN 42

Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2193
         (272 letters)



>NCBI__GCF_000092045.1:WP_042119745.1
          Length = 260

 Score = 87.0 bits (214), Expect = 4e-22
 Identities = 72/241 (29%), Positives = 100/241 (41%), Gaps = 8/241 (3%)

Query: 26  KNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRG-KHFSAGADLAWMQQSAELDYHTNL 84
           K NA +    R + L       DP LR  +I G G K F AG DL        +D    +
Sbjct: 22  KANAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAGWDLKAAASGDAVDGDYGV 81

Query: 85  DDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISACDMAIGADEAQFCLSEVRIGLA 144
                L EL      L  P +  V G   GG L +  + D+ I A+ A F L E+R G  
Sbjct: 82  GGFGGLQELR----DLNKPVICAVNGLCCGGGLEIALSTDLIIAAEHATFALPEIRSGTV 137

Query: 145 PAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLSESYPAEVLDQQVEQWIDNLLL 204
               S  + + I    A    LT    D   A   G ++E  PAE L ++  +    L  
Sbjct: 138 ADAASIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPAERLMERAWELARLLES 197

Query: 205 NSPAAMRASKELLREVGNGALTPALRRYTENAIA---RIRVSPEGQEGLRAFLQKRAPNW 261
             P    A KE++RE        A+ + T+   A   R+  S +  EG RAF +KR+P W
Sbjct: 198 GPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQLEGARAFAEKRSPIW 257

Query: 262 Q 262
           +
Sbjct: 258 K 258


Lambda     K      H
   0.318    0.133    0.382 

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: 120
Number of extensions: 5
Number of successful extensions: 3
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: 272
Length of database: 260
Length adjustment: 25
Effective length of query: 247
Effective length of database: 235
Effective search space:    58045
Effective search space used:    58045
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 Apr 09 2024. 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