GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Rhizobium etli CFN 42

Align 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized)
to candidate WP_011423940.1 RHE_RS02885 enoyl-CoA hydratase/isomerase family protein

Query= SwissProt::Q5XIE6
         (385 letters)



>NCBI__GCF_000092045.1:WP_011423940.1
          Length = 350

 Score =  254 bits (648), Expect = 3e-72
 Identities = 147/346 (42%), Positives = 208/346 (60%), Gaps = 7/346 (2%)

Query: 33  ETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKA 92
           + +EV++ERRG AG+I LNRP+ LN+L+L MIR I   L  + RD +   ++  G G + 
Sbjct: 2   QDSEVIIERRGTAGIIRLNRPRALNSLTLAMIRTITEALDGFARDAEVATVVATGEGERG 61

Query: 93  FCAGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVH 152
           FCAGGDI+AL E+ +AG  L+   +REE+ LN+ IA   KPYVAL+DGITMGGGVGLS H
Sbjct: 62  FCAGGDIRALHESARAGDGLAGTFWREEFRLNHMIAVYPKPYVALMDGITMGGGVGLSSH 121

Query: 153 GQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGIA 212
           G+ R+ TER+  AMPETGIG  PDVG  + LP+  G+ G +L LTG  +   D   A +A
Sbjct: 122 GRHRIVTERTRLAMPETGIGYVPDVGATWLLPKAPGEAGTWLGLTGLDIAAADAIYAHLA 181

Query: 213 THFVDSEKLHVLEEELLAL-KSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCF 271
              + S +L  + E L  L +  S+ DV GVL+ Y      G+ +      +   I+  F
Sbjct: 182 DLQIASSRLAEVIETLSGLPRGSSSGDVDGVLQVY--AEPPGESR---LRHNSTMIDRAF 236

Query: 272 SANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEG-STKTLQEVLTMEYR 330
             ++VE+IL  L  +   FA E  +V+   SPTSLK+ L+ L  G  + +L E L  E  
Sbjct: 237 RFDSVEEILAALAGEDGEFAAETRRVLLTRSPTSLKLALQLLRAGRRSGSLAECLGRELG 296

Query: 331 LTQACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFK 376
                ++  DF EG+RA +IDKD+ PKW PA ++ V  + + ++ K
Sbjct: 297 ACLQMLDNPDFFEGIRAAVIDKDRNPKWSPASVEAVKAQTVENFLK 342


Lambda     K      H
   0.320    0.136    0.394 

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: 291
Number of extensions: 12
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: 385
Length of database: 350
Length adjustment: 30
Effective length of query: 355
Effective length of database: 320
Effective search space:   113600
Effective search space used:   113600
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 Apr 09 2024. 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