GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutG in Herbaspirillum seropedicae SmR1

Align Formimidoylglutamase; EC 3.5.3.8; Formiminoglutamase; Formiminoglutamate hydrolase (uncharacterized)
to candidate HSERO_RS08555 HSERO_RS08555 agmatinase

Query= curated2:Q9KBE3
         (319 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS08555 HSERO_RS08555 agmatinase
          Length = 317

 Score =  112 bits (279), Expect = 2e-29
 Identities = 83/277 (29%), Positives = 132/277 (47%), Gaps = 11/277 (3%)

Query: 38  GLIGAPLSKSSISHSGASFAPTVIRKCLHAFSTYSVE-EDLDLAQLKLTDLGDITMHVTD 96
           G +G PL   + + SG  F P  IR        Y++         LK+ DLGD+ ++   
Sbjct: 38  GFVGVPLDIGTSNRSGTRFGPRQIRTESVLLRPYNMATRAAPFDSLKVADLGDVALNPYS 97

Query: 97  IVGSQARIEETMTKLLENEQNWQPIVLGGDHSISFPSIKAFASAKGTIGVIQFDAHHDLR 156
           ++ S   IEE   ++       + I LGGDH+++ P ++A A  +G +G+I  DAH D+ 
Sbjct: 98  LLDSVRMIEEAYDRIYAT--GCKTISLGGDHTLTLPILRALARYRGPVGLIHVDAHADVN 155

Query: 157 NLEDGGP-CNGTPFRSLLETGSLVGEHLVQIGIRDFSNSYPYRKYAEKHGVKVYTMKDVN 215
           +  +G    +GTPFR   E G L  + +VQIG+R          +    G +V   ++  
Sbjct: 156 DTMNGEKIAHGTPFRRAFEEGLLDPQRVVQIGLRGTGYHADDFDWCRAQGFRVVQAEECW 215

Query: 216 ARGLLTILDEAVAKLKRSVDVIYVSVDMDVLDQAHAPGCPAIGPGGMDSTTLLQG--IFH 273
            R L  +++E  A++      +Y++ D+D LD A APG      GG+   T+ QG  I  
Sbjct: 216 HRSLAPLMEEVRAQM--GDGPVYLTFDIDGLDPAFAPGTGTPEIGGL---TVQQGLEIIR 270

Query: 274 LGKDSLVQGMDIVEVDPTLDFREMTSRAAAHVILNYL 310
             K   +   D+VEV P  D    T+  AA++    L
Sbjct: 271 GCKGLDIVSADVVEVSPPYDQAGTTALVAANLAYEML 307


Lambda     K      H
   0.319    0.138    0.408 

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: 275
Number of extensions: 19
Number of successful extensions: 6
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: 319
Length of database: 317
Length adjustment: 27
Effective length of query: 292
Effective length of database: 290
Effective search space:    84680
Effective search space used:    84680
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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