GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuD in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_068173905.1 HTA01S_RS16835 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_4510
         (258 letters)



>NCBI__GCF_001592305.1:WP_068173905.1
          Length = 280

 Score =  110 bits (275), Expect = 3e-29
 Identities = 88/238 (36%), Positives = 119/238 (50%), Gaps = 19/238 (7%)

Query: 30  RAVATAAKGLPVLIPSLADLFPPSDILDALDGILLTGSPSNVEPFHYQGPASAPGTAHDP 89
           RA+A     +    P  A+  P ++++D LDG++L G   ++ P  Y      P  A D 
Sbjct: 41  RAIALMVPFIDEESPLSANRAPMTELVDLLDGLVLQGG-IDICPETYGDTLRDPAWAGDA 99

Query: 90  ARDATTLPLIRAAVDAGIPVLGICRGFQEMNVAFGGSLHQKV--HEVGTFIDHREDDTQA 147
            RD   L L+R  + AG PVLG+CRG Q +NV FGGSL Q +     GT I H+  DT  
Sbjct: 100 VRDRYELNLLRGFIAAGKPVLGVCRGAQLINVYFGGSLVQDIPSQRPGT-IQHQ--DTTR 156

Query: 148 VDVQYGPAHAVHIQPGGVLA---GLGLPQRIEVNSIHSQGIERLAPGLRAEAV-APDGLI 203
            D      H VH + G  L    G  +P R  V SIH Q ++RL  GL  EAV + DG+I
Sbjct: 157 YD---RLTHEVHFETGSSLQRLYGNSVPHR--VTSIHHQCVDRLGEGLVVEAVSSKDGII 211

Query: 204 EAVSVPGGKAFALGVQWHPEWEVSSNPHYLAIFQA---FGDACRARAAQRDADASNNA 258
           EA+    G  + LGVQWHPE+ ++       +  +     D  RA  A+ D   S  A
Sbjct: 212 EAIR-HTGPGYVLGVQWHPEFHLTPGEEMQGLLDSGPMMMDFLRAALARADRHQSGAA 268


Lambda     K      H
   0.319    0.136    0.413 

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: 249
Number of extensions: 21
Number of successful extensions: 4
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: 258
Length of database: 280
Length adjustment: 25
Effective length of query: 233
Effective length of database: 255
Effective search space:    59415
Effective search space used:    59415
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 (21.7 bits)
S2: 47 (22.7 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