GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Sinorhizobium meliloti 1021

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate SM_b20753 SM_b20753 acyl-CoA dehydrogenase

Query= BRENDA::B5UB85
         (416 letters)



>FitnessBrowser__Smeli:SM_b20753
          Length = 380

 Score =  249 bits (637), Expect = 8e-71
 Identities = 142/380 (37%), Positives = 219/380 (57%), Gaps = 7/380 (1%)

Query: 33  FGLSEEQQQLRKMVFDFAQKELAPKAAEIDKENNFKELRPFWKKLGDLGLLGITASSDYG 92
           F LSEEQ+ +R M  DFA+ E+AP A + D++ +F       +    LG+ GI    D G
Sbjct: 3   FRLSEEQEAIRTMALDFARDEIAPHAVDWDQQKHFPV--ETLRAAAALGMAGIYIRDDVG 60

Query: 93  GTGGKYSDHCVIMEELSRASGGIALSYGAHSNLCVNQINRNGTEEQKSKYLPKLCSGEHI 152
           GTG    D  +I+E L+     IA     H N+C   I+R GT+EQ+ + LP L + + +
Sbjct: 61  GTGLTRLDAAMIIEALATGCPAIASFVSIH-NMCAGMIDRYGTDEQRRRLLPPLLTMDVL 119

Query: 153 GALAMSEPGSGSDVVSMKLRAEKKGDYYVLNGNKFWITNGPDADVLVVYAKTNWSTSKQQ 212
            +  ++EPGSGSD  ++K RA ++GD Y+L G K +I+   ++ + +V A+T     K  
Sbjct: 120 ASYCLTEPGSGSDAAALKTRAVREGDAYLLTGQKQFISGAGESGLYIVMARTGEEGPK-- 177

Query: 213 HGISAFLIEKDYPGFSTAQKLDKLGMRGSNTGELVFEDCKVPAANLLGQENKGVYVLMSG 272
            GISAF++EKD PG +      K+G     T  ++ ++ +V   N LG E +G  + M+G
Sbjct: 178 -GISAFVVEKDAPGLTFGANEKKMGWHAQPTRAVMLDNVRVSVENRLGAEGEGFRIAMAG 236

Query: 273 LDLERLVLAAGPVGLMQAAIDTAFLYAHTRKQFGKNIGEFQLIQGKMADMYTTLSACRSY 332
           LD  RL +AA  +G  Q+A D A  Y   R+ FGK IGEFQ +Q ++ADM T L   R++
Sbjct: 237 LDGGRLSIAAASLGGAQSAFDKALAYVQERRAFGKAIGEFQALQFRLADMATDLEIARTF 296

Query: 333 LYNVAKACDNGHVN-SKDCAGVILYCAEKATQVALDAIQILGGNGYINDYPTGRILRDAK 391
           L+  A A D      +K CA    +  ++   VA DA+Q+ GG GY+ DY   +I+RD +
Sbjct: 297 LWRAACALDAADPEATKLCAMAKRFVTDRCFSVANDALQLHGGYGYLADYGVEKIVRDLR 356

Query: 392 LYEIGAGTSEVRRMLIGRAL 411
           +++I  GT+E+ R+++ RA+
Sbjct: 357 VHQILEGTNEIMRLIVSRAI 376


Lambda     K      H
   0.318    0.135    0.399 

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: 366
Number of extensions: 19
Number of successful extensions: 5
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: 416
Length of database: 380
Length adjustment: 31
Effective length of query: 385
Effective length of database: 349
Effective search space:   134365
Effective search space used:   134365
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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