GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Acidovorax sp. GW101-3H11

Align 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized)
to candidate Ac3H11_4470 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)

Query= curated2:P77161
         (292 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4470
          Length = 304

 Score =  157 bits (396), Expect = 4e-43
 Identities = 93/289 (32%), Positives = 148/289 (51%), Gaps = 6/289 (2%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHV------TTIGPVADELLSLGAVSVETARQVTEA 55
           K+ F+GLG+MG PMA +LA AGH++ V       ++   A+   +       T R+    
Sbjct: 16  KVAFLGLGVMGYPMAGHLALAGHEVTVYNRTATKSVAWCAEYAGAKAPKHATTPREAAAG 75

Query: 56  SDIIFIMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYL 115
           +DI+F  V +   +  V  G +G       G   VD ++ S    +        LG  ++
Sbjct: 76  ADIVFCCVGNDNDLRSVTLGADGAFAGMQPGAIFVDHTTASAEVARELYAAAKALGLQFV 135

Query: 116 DAPVSGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQII 175
           DAPVSGG+ GA+ G L++M GGD A F+  +P+     +  TL+G +G GQ  K+ NQI 
Sbjct: 136 DAPVSGGQAGAQNGQLTVMCGGDAAAFDAAQPVATAFSRAFTLLGESGSGQLAKMVNQIC 195

Query: 176 VALNIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALH 235
           +A  ++ +SEA+ F   AG D  +V   +  G A S  ++  G+ M+   F+ GF +   
Sbjct: 196 IAGLVQGLSEAVAFGQNAGLDMKQVLDVIGKGAAQSWQMDNRGKTMVDGKFDFGFAVDWM 255

Query: 236 QKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALE 284
           +KDL L L  AK     +P TA   + +      GG++ D S+L++ L+
Sbjct: 256 RKDLGLVLDEAKRNGSRVPVTALVDQFYADVQQMGGNRWDTSSLIKRLK 304


Lambda     K      H
   0.318    0.135    0.376 

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: 12
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: 292
Length of database: 304
Length adjustment: 26
Effective length of query: 266
Effective length of database: 278
Effective search space:    73948
Effective search space used:    73948
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 (21.7 bits)
S2: 48 (23.1 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