GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Amantichitinum ursilacus IGB-41

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_053939623.1 WG78_RS20115 FAD-binding oxidoreductase

Query= reanno::pseudo5_N2C3_1:AO356_21495
         (427 letters)



>NCBI__GCF_001294205.1:WP_053939623.1
          Length = 428

 Score =  319 bits (817), Expect = 1e-91
 Identities = 171/418 (40%), Positives = 252/418 (60%), Gaps = 6/418 (1%)

Query: 9   SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68
           S+Y AS    P   ALQ  ++ DVC++GAGY+GLS+AL L + GF V VLEA +V +GAS
Sbjct: 12  SWYEASVTRPPADAALQGALDVDVCIVGAGYSGLSAALELRQRGFSVAVLEAEQVAWGAS 71

Query: 69  GRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVF 128
           GRNGGQ++  ++ D D + R +GP  A+   +++  G  ++  RVA+Y I CDL  G + 
Sbjct: 72  GRNGGQVLVGFAND-DTVLRQLGPAAARQAWDISVAGVHLLHARVARYGIDCDLVRGYLH 130

Query: 129 AALTAKQ---MGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHP 185
            A +A++   + H  +Q R  + FG+  +  +  + +R  +    YVG   D   GHIHP
Sbjct: 131 VATSARKAEGLRHWTAQMR--DTFGYDPISDIAPKDVRNWIDSPRYVGAAHDALSGHIHP 188

Query: 186 LNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVP 245
           L  ALG A A    G  ++  S   RIE G    +HT QG+VR++F ++A NAY+G L+ 
Sbjct: 189 LKYALGLADAARQAGVQLFAHSAVSRIEHGPLVTLHTAQGRVRSRFALIAANAYVGQLLG 248

Query: 246 ELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVY 305
           +  A+ MP  + +IATEPL  E A +L+     V D N+++DY+RL+ D R++FGG V  
Sbjct: 249 KTGARIMPVRSFIIATEPLPPEQAQALIRGRAAVCDTNFMIDYFRLSADGRVLFGGRVTS 308

Query: 306 GARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCS 365
           G   P  +   +R ++   FPQL  V I +AW G   +T++R P  GR+  N+YY QG  
Sbjct: 309 GNAGPDALMPSLRARLAGVFPQLAHVAITHAWGGLVDVTMNRAPDFGRIAPNVYYLQGFC 368

Query: 366 GHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423
           GHGV  T +AG+++AEA+ GQAERFD FA L H+ +PGG  L + +  +G  Y  L++
Sbjct: 369 GHGVALTGMAGQLVAEAIAGQAERFDLFARLQHHRYPGGPGLHSTWLRLGVAYNQLKE 426


Lambda     K      H
   0.320    0.139    0.421 

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: 491
Number of extensions: 18
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: 427
Length of database: 428
Length adjustment: 32
Effective length of query: 395
Effective length of database: 396
Effective search space:   156420
Effective search space used:   156420
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: 51 (24.3 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