GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Streptacidiphilus oryzae TH49

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate WP_037577556.1 BS73_RS29620 2-hydroxy-3-oxopropionate reductase

Query= SwissProt::P28811
         (298 letters)



>NCBI__GCF_000744815.1:WP_037577556.1
          Length = 296

 Score =  207 bits (527), Expect = 2e-58
 Identities = 128/289 (44%), Positives = 167/289 (57%), Gaps = 13/289 (4%)

Query: 4   IAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEVVIS 63
           IAF+GLG MG PMAANL+KAGH+V  ++    AV  LVE G + ADS      GAEVVI+
Sbjct: 6   IAFIGLGIMGRPMAANLVKAGHQVTGYNRSRPAVDALVEAGGRAADSVADAVRGAEVVIT 65

Query: 64  MLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAPVSG 123
           MLPA   V  +  G+DG+LA  A   LLID STI P+T+  V E AA +G+  LDAPVSG
Sbjct: 66  MLPADPEVTEVVTGEDGVLAHAAEGTLLIDMSTITPQTSLAVQETAAPRGVRTLDAPVSG 125

Query: 124 GVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGILMA 183
           G  GA  G LS +VGG AE  A ARPVLE +G  I H G HGAGQ  K  N +++   + 
Sbjct: 126 GEAGAVEGVLSIMVGGDAEDVAEARPVLEALGTTIVHVGPHGAGQTVKAANQLIVASNIQ 185

Query: 184 GTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASN-GYAGGFQVR 242
             AEA+    ++G+D A   +V+     G+  LN          +A   N  +  GF++ 
Sbjct: 186 ALAEAVVFLERSGVDLASALDVLGGGLAGSTVLN--------RKRANILNRDFKPGFRID 237

Query: 243 LMNKDLGLALANAQAVQASTPLGALARNLF-SLHAQADAEHEGLDFSSI 290
           L +KD+G+    A+AV A  P+GAL   L  S  +  D    GLD S++
Sbjct: 238 LHHKDMGIVTDAARAVGAPLPVGALVAQLVASARSNGDG---GLDHSAL 283


Lambda     K      H
   0.317    0.135    0.395 

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: 282
Number of extensions: 15
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: 298
Length of database: 296
Length adjustment: 26
Effective length of query: 272
Effective length of database: 270
Effective search space:    73440
Effective search space used:    73440
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 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