GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ligK in Cupriavidus basilensis 4G11

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 RR42_RS27210 RR42_RS27210 hypothetical protein

Query= SwissProt::A5W059
         (238 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS27210 RR42_RS27210 hypothetical
           protein
          Length = 237

 Score =  283 bits (723), Expect = 3e-81
 Identities = 143/226 (63%), Positives = 167/226 (73%)

Query: 10  IVVRNIQRAELDSIDALGRLGVATVHEAQNRKGLLSSKMRPIQQGTSLAGSAVTVLVAPG 69
           I  RNI RA    IDALG  GVATVHEAQ R GL+   MRP+Q   ++AGSAVTVL+ PG
Sbjct: 4   IAYRNILRAAAADIDALGAAGVATVHEAQRRTGLMKPYMRPVQSRAAMAGSAVTVLMHPG 63

Query: 70  DNWMFHVAVEQCRPGDVLVVSPSSPCTDGYFGDLLATSLQARGVRALIVDAGVRDTQTLR 129
           DNWM HVAVE  +PGDVLVV+  S CTDG FGDLLATSL+ARG R L++DAGVRD  TL 
Sbjct: 64  DNWMIHVAVEMVQPGDVLVVALVSDCTDGLFGDLLATSLKARGARGLVIDAGVRDVSTLN 123

Query: 130 DMGFAVWARAINAQGTVKETLGSVNLPVICGGQLINPGDIVVADDDGVVVVRRDECESTL 189
            MGF VW+RA++AQG VKET+G+VN+PV+C G  + PGD++VADDDGVVVV R     T 
Sbjct: 124 AMGFPVWSRAVSAQGAVKETVGAVNVPVVCAGAHVRPGDVIVADDDGVVVVPRPLAAETA 183

Query: 190 VAAAERAGLEEEKRLRLAAGELGLDIYKMRERLEAKGLRYVDNIED 235
             AAER  +EE KR  LAAG LGLD+Y+MRE L AKGL Y +   D
Sbjct: 184 RRAAERGAMEEGKRATLAAGVLGLDMYQMREALAAKGLAYAEQTVD 229


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: 195
Number of extensions: 4
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: 237
Length adjustment: 23
Effective length of query: 215
Effective length of database: 214
Effective search space:    46010
Effective search space used:    46010
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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