GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Methanospirillum lacunae Ki8-1

Align glucosamine-1-phosphate N-acetyltransferase (EC 2.3.1.157); galactosamine-1-phosphate N-acetyltransferase (EC 2.3.1.276); UDP-N-acetylglucosamine diphosphorylase (EC 2.7.7.23); glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24); aldose-1-phosphate nucleotidyltransferase (EC 2.7.7.37); UDP-N-acetylgalactosamine diphosphorylase (EC 2.7.7.83); UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate WP_109968441.1 DK846_RS08100 sugar phosphate nucleotidyltransferase

Query= BRENDA::Q975F9
         (401 letters)



>NCBI__GCF_003173355.1:WP_109968441.1
          Length = 401

 Score =  255 bits (652), Expect = 1e-72
 Identities = 155/402 (38%), Positives = 234/402 (58%), Gaps = 27/402 (6%)

Query: 1   MKAFILAAGSGERLEPITHTRPKAFVPILSKPLIEYQIEYLRKCGIRDITVIVSSKNKEY 60
           ++  ILAAG G+R+ P+T +RPK  +P+ ++P++E+ I  +R CGI +  ++V      Y
Sbjct: 2   VQCVILAAGEGKRMRPLTGSRPKVMIPVANRPMLEHLINAIRDCGINEFVLVVG-----Y 56

Query: 61  FEKKLKE-----------ISIVTQKDDIKGTGAAILS--AKFNDEALIIYGDLFFSNEKE 107
            E  ++            I  VTQK   +GTG A+L+  +  N + L++ GD+  S E +
Sbjct: 57  HEAAVRHHFGDGSDFGVSIRYVTQKRQ-RGTGDAVLNVLSHVNGDFLLLNGDMILSRE-D 114

Query: 108 ICNIITLKENAIIGVKVSNPKDYGVLVLDNQNNLSKIIEKPEIPPSNLINAGIYKLNSDI 167
           I  +++    A+   K  +P+D+GV+ + +   ++   EK E P S+LINAG+Y  N D+
Sbjct: 115 IKAVLSSPSPALGICKSDHPRDFGVVTVKD-GIITGFEEKSENPKSDLINAGLYLFNYDL 173

Query: 168 FTYLDKISISERGELELTDAINLMAKDHRVKVIEYEGYWMDIGKPWNIIDVNKWALDNLV 227
           F++L  I+ S RGELELTDA+    K   +  +     W D+G PW+++  N+  L +L 
Sbjct: 174 FSHLKLITPSPRGELELTDALLPYIKAGSLHAVMLSS-WADMGSPWDLLTANEVLLVSLS 232

Query: 228 FSQNLGNVEDNVKIKGKVIIEEDAEIKSGTYIEGPVYIGKGSEIGPNSYLRPYTILVEKN 287
            S   G +ED V +KG V + +   +K+GTYIEGP  IGK   IGP++Y+R  T + +  
Sbjct: 233 -SCIEGEIEDGVVLKGAVQVGKGTVVKAGTYIEGPCVIGKDCRIGPHAYIRGATAIGDNC 291

Query: 288 KIGASVEVKESVIMEGSKIPHLSYVGDSVIAEDVNFGAGTLIANLRFDEKEVKVNVKGKR 347
            IG S+E+K S++M  S IPH +YVGDSVIA   NFGAGT IANLR D+K +        
Sbjct: 292 HIGHSIELKNSIVMNHSNIPHFNYVGDSVIASGCNFGAGTKIANLRHDKKCISAG----G 347

Query: 348 ISSGRRKLGAFIGGHVRTGINVTILPGVKIGAYARIYPGAVV 389
           +++ R+K GA IG  V  GIN ++  G  IG   RI P   V
Sbjct: 348 VNTRRKKFGAVIGDDVLFGINCSVNVGAVIGNRCRIAPHCFV 389


Lambda     K      H
   0.317    0.139    0.393 

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: 453
Number of extensions: 23
Number of successful extensions: 8
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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: 50 (23.9 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