GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Herbaspirillum seropedicae SmR1

Align Succinyl-CoA:3-ketoacid coenzyme A transferase subunit A; Succinyl-CoA:3-oxoacid CoA-transferase; OXCT A; EC 2.8.3.5 (characterized)
to candidate HSERO_RS20000 HSERO_RS20000 3-oxoadipate CoA-transferase subunit A

Query= SwissProt::P56006
         (232 letters)



>FitnessBrowser__HerbieS:HSERO_RS20000
          Length = 224

 Score =  221 bits (563), Expect = 9e-63
 Identities = 105/223 (47%), Positives = 159/223 (71%), Gaps = 2/223 (0%)

Query: 1   MNKVITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSNNCGVDDFG 60
           +NK+   L++A++ + DG TI++GGFG  G+P   ID +  +G +DL +V+NN G  + G
Sbjct: 2   INKISDSLEQAVADIHDGATIMIGGFGNAGMPSALIDALIAQGARDLTIVNNNAGNGETG 61

Query: 61  LGILLEKKQIKKIIASYV--GENKIFESQMLNGEIEVVLTPQGTLAENLHAGGAGIPAYY 118
           L  LL+ K++KKI+ S+    ++++F++   +GEIE+ LTPQG LAE + A GAGI  ++
Sbjct: 62  LAALLKTKRVKKIVCSFPRQSDSQVFDALYRSGEIELELTPQGNLAERIRAAGAGIGGFF 121

Query: 119 TPTGVGTLIAQGKESREFNGKEYILERAITGDYGLIKAYKSDTLGNLVFRKTARNFNPLC 178
           +PTG GT++A+GKE+RE NG+ Y+LE  I  D+ LIKA + D  GNLV+RKTARNF P+ 
Sbjct: 122 SPTGYGTMLAEGKETREINGRHYVLESPIHADFALIKALRGDRWGNLVYRKTARNFGPIM 181

Query: 179 AMAAKICVAEVEEIVPAGELDPDEIHLPGIYVQHIYKGEKFEK 221
           AMAAK  +A+V E+V  G+LDP+ I  PGI+VQ I + ++ ++
Sbjct: 182 AMAAKCTIAQVSEVVELGQLDPENIVTPGIFVQRIVQTKEAQQ 224


Lambda     K      H
   0.317    0.140    0.400 

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: 166
Number of extensions: 7
Number of successful extensions: 2
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: 232
Length of database: 224
Length adjustment: 23
Effective length of query: 209
Effective length of database: 201
Effective search space:    42009
Effective search space used:    42009
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 (21.6 bits)
S2: 46 (22.3 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