GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Geotalea uraniireducens Rf4

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_011939638.1 GURA_RS14190 D-2-hydroxyacid dehydrogenase

Query= curated2:B1L765
         (332 letters)



>NCBI__GCF_000016745.1:WP_011939638.1
          Length = 330

 Score =  177 bits (448), Expect = 4e-49
 Identities = 115/296 (38%), Positives = 163/296 (55%), Gaps = 13/296 (4%)

Query: 30  DEAPPSKKVIIERVKDCDALVSLLTDPIDAEVFEAAPKLRIVAQYAVGYDNIDVKEATKR 89
           D  PP  K  +ER +D + ++ L    +DA+  +A PKLR ++  A GY+N+DV  A   
Sbjct: 35  DRTPPELK--LERARDAE-IILLSKVKLDADTLKALPKLRYISLLATGYNNVDVAAAGAL 91

Query: 90  GIYVTNTPGVLTETTADFAFALLMAAARRVVEADRYVREGKW-----KVAWHPMMMLGYD 144
           GI V+N P   TE+ A   FALL+  A  V   D  V+ G+W        W   ++   +
Sbjct: 92  GIPVSNVPAYSTESVAQTTFALLLELAVNVGVHDAAVKAGEWIRCPDHSFWKAPIV---E 148

Query: 145 VYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDF 204
           + G T+GIVG G IG AVAR A  FGMR++ Y     +D    + V +VPLE+L   +D 
Sbjct: 149 LNGLTIGIVGYGVIGKAVARIAAAFGMRVIAYAPRIPQD-AGPVPVSFVPLEELFAIADV 207

Query: 205 VSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVF 264
           V+L+ P T E    +    L  MK  A L+N +RG +V++  L  AL+ G IAGA LDV 
Sbjct: 208 VTLNCPQTPENTGFVNSRLLGCMKPGAFLINVARGGLVNEADLAHALRSGQIAGAALDVV 267

Query: 265 EQEPIPPDDPLLKLENVVLAPHAASASHETRSRMAEMVAENLIAFKRGEIPPNLVN 320
             EP+  ++PLL   N +  PH A AS   R R+ ++VA N+ +F  G  P N+VN
Sbjct: 268 AHEPMLAENPLLSAPNCIFTPHIAWASLAARRRLMDIVAANVASFLGGS-PINVVN 322


Lambda     K      H
   0.319    0.137    0.398 

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: 240
Number of extensions: 12
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: 332
Length of database: 330
Length adjustment: 28
Effective length of query: 304
Effective length of database: 302
Effective search space:    91808
Effective search space used:    91808
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 (21.8 bits)
S2: 49 (23.5 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