GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligK in Rhizobium etli CFN 42

Align 4-hydroxy-4-methyl-2-oxoglutarate aldolase/4-carboxy-4-hydroxy-2-oxoadipate aldolase; HMG/CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate WP_011427805.1 RHE_RS23745 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

Query= SwissProt::A5W059
         (238 letters)



>NCBI__GCF_000092045.1:WP_011427805.1
          Length = 224

 Score =  174 bits (440), Expect = 2e-48
 Identities = 89/212 (41%), Positives = 132/212 (62%)

Query: 16  QRAELDSIDALGRLGVATVHEAQNRKGLLSSKMRPIQQGTSLAGSAVTVLVAPGDNWMFH 75
           +R +  +I+A+ +   AT+HEAQ R+G LSS+++P+     L G A TV  AP DN M  
Sbjct: 9   ERPDKAAIEAVSKFSPATIHEAQGRRGALSSRLKPVDYRMKLCGPAFTVKCAPRDNIMLQ 68

Query: 76  VAVEQCRPGDVLVVSPSSPCTDGYFGDLLATSLQARGVRALIVDAGVRDTQTLRDMGFAV 135
           +A+   +PGD++VVS       G FGD+LA +  A+G+  L+ D GVRDT  LR++GF V
Sbjct: 69  LAINYAKPGDIIVVSAGEYEEAGSFGDVLANACLAKGIGGLVTDTGVRDTLQLRELGFPV 128

Query: 136 WARAINAQGTVKETLGSVNLPVICGGQLINPGDIVVADDDGVVVVRRDECESTLVAAAER 195
           ++ ++  +GTVKET+ +VN P+I GG+ INPGDI+V D DG+VVVRR E +     +  R
Sbjct: 129 FSLSVCIKGTVKETIAAVNDPIIVGGETINPGDIIVGDADGLVVVRRQEAQEAARLSQAR 188

Query: 196 AGLEEEKRLRLAAGELGLDIYKMRERLEAKGL 227
              E        AG+  +++  +   L+AKGL
Sbjct: 189 EDAEAGYITAYKAGKSVIEVSNLAPVLKAKGL 220


Lambda     K      H
   0.318    0.136    0.390 

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: 145
Number of extensions: 5
Number of successful extensions: 1
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: 238
Length of database: 224
Length adjustment: 23
Effective length of query: 215
Effective length of database: 201
Effective search space:    43215
Effective search space used:    43215
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: 46 (22.3 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