GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Rhizobium leguminosarum bv. trifolii WSM1325

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_012756545.1 RLEG_RS04380 SDR family oxidoreductase

Query= BRENDA::Q84X95
         (319 letters)



>NCBI__GCF_000023185.1:WP_012756545.1
          Length = 266

 Score =  112 bits (279), Expect = 1e-29
 Identities = 73/193 (37%), Positives = 111/193 (57%), Gaps = 12/193 (6%)

Query: 54  AIITGPTDGIGKAFAFQLAQKGLHLVLVARNPDKLKAVSDSIQAKHSTTQIKTVLMDFSG 113
           A++TG + GIG  +A +LA+KG  L+LVAR  D+LKA+SD + A H  T+++ V  D + 
Sbjct: 10  ALVTGASAGIGAIYAARLAEKGYDLILVARRADRLKALSDKLGAAHG-TKVEVVEADLTK 68

Query: 114 DIDAGVRRIKEAI-EGLEVGILINNAGVS--YPYAKYFHEVDEELLGNLIKINVEGTTKV 170
           D D  V R+++ + E   + +L+NNAG S   P AK      EE    +I +NV   T++
Sbjct: 69  DAD--VNRVEKVLKENSAITLLVNNAGNSTLAPVAK----TTEEDAAAMIALNVTALTRL 122

Query: 171 TQAVLVNMLKRKRGAIVNMGSGAAALIPSYPFYSVYAGAKTYVDQFSRCLHVEYKKSGID 230
           T AVL   L R  GAI+N+ S       + P  ++Y+G K YV  FSR L  E  ++ + 
Sbjct: 123 THAVLPAFLSRNHGAIINVAS--VLSFHALPISAIYSGTKGYVMNFSRGLQQELAETNVR 180

Query: 231 VQCQVPLYVATKM 243
           +Q  +P   AT++
Sbjct: 181 LQLVMPAATATEL 193


Lambda     K      H
   0.322    0.137    0.402 

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: 156
Number of extensions: 8
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: 319
Length of database: 266
Length adjustment: 26
Effective length of query: 293
Effective length of database: 240
Effective search space:    70320
Effective search space used:    70320
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 (21.9 bits)
S2: 48 (23.1 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