GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Rhizobium etli CFN 42

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011428126.1 RHE_RS25445 acyl-CoA dehydrogenase

Query= BRENDA::Q9SWG0
         (409 letters)



>NCBI__GCF_000092045.1:WP_011428126.1
          Length = 395

 Score =  202 bits (515), Expect = 1e-56
 Identities = 126/367 (34%), Positives = 190/367 (51%), Gaps = 7/367 (1%)

Query: 39  KESVSKFAQDNIAPHAERIDKTNSFPKDVNLWKLMGEFNLHGITAPEEYGGLGLGYLYHC 98
           +++   +AQ  +AP    +D   +   D  +++ MGE  L G T   EYGG GLGY  + 
Sbjct: 28  QDTAHAYAQQKLAPRV--LDAFRNEKTDPAIFREMGELGLLGPTISPEYGGAGLGYTAYG 85

Query: 99  IAMEEISRASGSVALSYGAHSNLCINQLVRNGTAAQKEKYLPKLISGEHVGALAMSEPNA 158
           +   E+ R            S+L +  +   G+AAQK+KYLPKL +GE +G   ++EP+ 
Sbjct: 86  LIAREVERVDSGYRSMMSVQSSLVMVPIETFGSAAQKQKYLPKLATGEWIGCFGLTEPDH 145

Query: 159 GSDVVGMKCKAEKVDGGYILNGNKMWCTNGPSAETLVVYAKTDTKAGSKGITAFIIEKGM 218
           GSD   M  +A+KVDGGY L G+K W +N P A+  VV+AKT+       I  FI+EKG 
Sbjct: 146 GSDPGSMATRAKKVDGGYSLTGSKTWISNAPIADVFVVWAKTEDGL----IRGFILEKGW 201

Query: 219 TGFSTAQKLDKLGMRGSDTCELVFENCFVPEENILDKEGKGVYVLMSGLDLERLVLAAGP 278
            G S      K+G+R S T E+V +  FVPEEN+L     G+    + L+  R  +A G 
Sbjct: 202 KGLSAPAIHGKVGLRASITGEVVMDGVFVPEENLLPGV-TGLKGPFTCLNSARFGIAWGA 260

Query: 279 LGIMQACLDNVLPYIRQREQFGRPVGEFQFIQGKVADMYTALQSSRSYVYSVARDCDNGK 338
           LG  + C      Y+ +R+QFGRP+   Q IQ K+ADM   +         + R  + G 
Sbjct: 261 LGAAEDCYARARQYVLERKQFGRPLAANQLIQKKLADMAAEIALGLQGCLRLGRMKEEGH 320

Query: 339 VDPKDCAGTILCAAERATQVALQAIQCLGGNGYINEYATGRLLRDAKLYEIGAGTSEIRR 398
              +  +     +  +A ++A  A   LGGNG  +E+   R L + ++     GT +I  
Sbjct: 321 PPVELTSILKRNSCGKALEMARAARDMLGGNGISDEFGIARHLVNLEVVNTYEGTHDIHA 380

Query: 399 IVIGREL 405
           ++IGR +
Sbjct: 381 LIIGRSI 387


Lambda     K      H
   0.318    0.135    0.395 

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: 360
Number of extensions: 19
Number of successful extensions: 4
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: 409
Length of database: 395
Length adjustment: 31
Effective length of query: 378
Effective length of database: 364
Effective search space:   137592
Effective search space used:   137592
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: 50 (23.9 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