GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligK in Azospirillum brasilense Sp245

Align 4-carboxy-4-hydroxy-2-oxoadipate aldolase; CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate AZOBR_RS26905 AZOBR_RS26905 hypothetical protein

Query= SwissProt::G2IQQ8
         (228 letters)



>FitnessBrowser__azobra:AZOBR_RS26905
          Length = 223

 Score =  310 bits (795), Expect = 1e-89
 Identities = 161/223 (72%), Positives = 181/223 (81%)

Query: 6   MGVVVQNIERAPLEVIDGLAACGVATVHEAQGRTGLLASYMRPIYRGARVAGSALTISAP 65
           M VVVQ IERA   VI GLA CGVATVHEAQGR GLLAS +RPIY GA+ A SA+TI AP
Sbjct: 1   MNVVVQTIERADPAVIAGLAECGVATVHEAQGRKGLLASALRPIYPGAQFAASAVTILAP 60

Query: 66  PGDNWMVHVAIEQLKAGDILLLAPTSPCEDGYFGDLLATSAQARGCRGLVIDAGVRDVRD 125
           P DNWM+HVAIEQ+K GD+L+LA TSP + GYFGDLLATSA+ARGC GLVIDAGVRDVR 
Sbjct: 61  PADNWMLHVAIEQVKPGDVLVLATTSPSDAGYFGDLLATSAKARGCAGLVIDAGVRDVRT 120

Query: 126 LTEMNFPVWSKAIYAQGTVKNTLGSVNVPVVCANALVNPGDVIVADDDGVCVVPLANAEK 185
           LT+M+FPVWS+A+ AQGTVK TLGSVNVPVVCA ALVNPGDVIVADDDGVCVV    A +
Sbjct: 121 LTDMSFPVWSRAVCAQGTVKETLGSVNVPVVCAGALVNPGDVIVADDDGVCVVRREEAAE 180

Query: 186 VLEAARAREANEGDKREKMANGVLGLDLYKMRERLEKEGLKYV 228
           VL  A+ R A E +KR ++A G LGLDLY MR  L  +GL+YV
Sbjct: 181 VLAKAQDRLAKEEEKRARLAAGELGLDLYGMRGPLAAKGLRYV 223


Lambda     K      H
   0.318    0.136    0.397 

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: 229
Number of extensions: 8
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: 228
Length of database: 223
Length adjustment: 22
Effective length of query: 206
Effective length of database: 201
Effective search space:    41406
Effective search space used:    41406
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:

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