GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Rhodobacter viridis JA737

Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate WP_110803876.1 C8J30_RS01040 3-hydroxyisobutyrate dehydrogenase

Query= SwissProt::P0ABQ2
         (294 letters)



>NCBI__GCF_003217355.1:WP_110803876.1
          Length = 290

 Score =  147 bits (370), Expect = 4e-40
 Identities = 104/298 (34%), Positives = 147/298 (49%), Gaps = 24/298 (8%)

Query: 1   MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQC--- 57
           MKVGFIGLG MG PM+ NL KAG+ ++  D        + A   E  + AK+IAE     
Sbjct: 1   MKVGFIGLGNMGAPMAANLAKAGHRVMGFD--------LAAPCPEGVAQAKSIAEAARGA 52

Query: 58  DVIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLD 117
           +V+ITMLPN   ++ VA   +  +    PG VL D S++   ++R+++      G+  LD
Sbjct: 53  EVVITMLPNGAILRLVA---DEALRAMTPGAVLCDCSTVDVESARQVAAEAATAGMGALD 109

Query: 118 APVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIV 177
           APVSGG   A  GTL+ MVGG  A F     L   M    VH G  GAG   K+ N +I+
Sbjct: 110 APVSGGVGGATAGTLTFMVGGSDAAFATVKPLFDVMGQKAVHCGASGAGQAAKICNNMIL 169

Query: 178 ALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAP-------MVMDRNFKPG 230
            + + A  EA  LA K G++   ++  +      S  ++A  P          D  +KPG
Sbjct: 170 GVTMIATCEAFALADKLGLDRAKMFDVVSTSSGYSWTMNAYCPAPGVGPKSPADNGYKPG 229

Query: 231 FRIDLHIKDLANALDTSHGVGAQLPL--TAAVMEMMQALRADGLGTADHSALACYYEK 286
           F  +L +KDL  +   + G  A  P+   AA +        DG G  D SA+   +EK
Sbjct: 230 FAAELMLKDLRLSQQAAEGADADTPMGALAAALYARFVEEEDGKG-MDFSAMLPRFEK 286


Lambda     K      H
   0.316    0.133    0.366 

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: 222
Number of extensions: 13
Number of successful extensions: 4
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: 294
Length of database: 290
Length adjustment: 26
Effective length of query: 268
Effective length of database: 264
Effective search space:    70752
Effective search space used:    70752
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 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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