GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS08555
          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.

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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