GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuD in Lactobacillus silagei IWT126

Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_089136150.1 CES79_RS01915 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein

Query= reanno::Koxy:BWI76_RS10705
         (254 letters)



>NCBI__GCF_002217945.1:WP_089136150.1
          Length = 239

 Score =  132 bits (332), Expect = 6e-36
 Identities = 86/242 (35%), Positives = 123/242 (50%), Gaps = 14/242 (5%)

Query: 5   MYKPVIGVVMCRNRLKGHQTQTLQEKYLNAIVNAGGVPIALPHALAEPELLSALLPKLDG 64
           M KP+IG+   R  + G    ++ +  + A+V AGGVP+ +P    E +L +     +DG
Sbjct: 1   MAKPIIGIPAERRLVDGSYLNSVNQGEVAAVVKAGGVPVLIP--TRESDLATNYSQLIDG 58

Query: 65  IYLPGSPSNVQPHLYGENGDEP-----DADPGRDLLSMALIDAALERRIPIFAICRGLQE 119
           + LPG   +V P  YGE   EP      +D   D   +AL + A+    PI  ICRG Q 
Sbjct: 59  LLLPGGV-DVAPRFYGE---EPLPKMAASDDRLDATEIALTNQAVTAGKPILGICRGTQV 114

Query: 120 LVVATGGTLYRRLFEQPELLEHREDPELPVEQQYAPSHEVQVQEGGLLSQLIPGCNTFWV 179
           L VA GG LY+ +  Q +   ++   +   +Q    +H + V EG LL  +  G     V
Sbjct: 115 LNVALGGNLYQDIGTQVDHQTYQHSQKASFDQG---THYIDVAEGSLLQGIFQGQQHVLV 171

Query: 180 NSLHGQGAKTTGPRLRVEARSPDGLAEAVSVNDHPFALGVQWHPEWNSSEYALSRMLFEG 239
           NSLH Q  KT  P+L++ A++ DG+ E V   D    + VQWHPE    E AL   +FE 
Sbjct: 172 NSLHHQAIKTPAPQLKITAKASDGIIECVESKDSNLIVAVQWHPELMFKEDALQFAIFED 231

Query: 240 FI 241
           FI
Sbjct: 232 FI 233


Lambda     K      H
   0.318    0.137    0.415 

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: 163
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: 254
Length of database: 239
Length adjustment: 24
Effective length of query: 230
Effective length of database: 215
Effective search space:    49450
Effective search space used:    49450
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: 46 (22.3 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