GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Streptacidiphilus oryzae TH49

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate WP_063836874.1 BS73_RS00355 NAD(P)-dependent oxidoreductase

Query= reanno::psRCH2:GFF2390
         (296 letters)



>NCBI__GCF_000744815.1:WP_063836874.1
          Length = 362

 Score =  127 bits (319), Expect = 4e-34
 Identities = 90/297 (30%), Positives = 145/297 (48%), Gaps = 15/297 (5%)

Query: 1   MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60
           + +G+IG G MGA MA  L +AGH L+V++   A  E L   GA   DS   +   + ++
Sbjct: 15  LRVGWIGTGRMGAAMAERLARAGHDLAVWNRTRAKAEPLRRFGAEVRDSIAELR--DRDV 72

Query: 61  IITMLPAAAHVKGVYLGVNGLI---AHSRAG---VMLIDCSTIDPHSAREVAKAAAEHGN 114
           + T +  +  +K V LG +GLI     + AG    +++DCST+   ++  V +A A  G 
Sbjct: 73  VFTTVAGSEDLKEVLLGEDGLIHSDGQAPAGPVPAVVVDCSTVSAEASAAVREACAAAGA 132

Query: 115 PMLDAPVSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVAN 174
             L APVSG      AG L+ +V G    ++   P+L  +G+   + G     ++ K+A+
Sbjct: 133 DFLAAPVSGNAKVVEAGKLSLVVSGPQKAYERVSPLLHTIGRAATYAGEGDTARLVKIAH 192

Query: 175 NMLLGISMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRG 234
           N+ LG+    +AE   L    G+        +N S     S+ T    P  +     +  
Sbjct: 193 NVFLGVVTQSLAEITVLAEKGGVPRHAFLEFLNDSV--LGSAFTRYKSPAFV-----NLD 245

Query: 235 YSGGFGSDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAIINQ 291
           YS  F   L+ KDL L  +AA+++  P+ L A   QL Q+    G  G DF+ +++Q
Sbjct: 246 YSPTFTPPLLRKDLDLGLDAARELGVPMPLAAATAQLVQATIGGGRTGEDFAVLLDQ 302


Lambda     K      H
   0.318    0.134    0.392 

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: 288
Number of extensions: 9
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: 296
Length of database: 362
Length adjustment: 28
Effective length of query: 268
Effective length of database: 334
Effective search space:    89512
Effective search space used:    89512
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