GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocF in Pseudomonas putida KT2440

Align Arginase 1, mitochondrial; Agmatinase ARGAH1; Arginine amidohydrolase 1; EC 3.5.3.1; EC 3.5.3.11 (characterized)
to candidate PP_4523 PP_4523 putative Agmatinase

Query= SwissProt::P46637
         (342 letters)



>FitnessBrowser__Putida:PP_4523
          Length = 320

 Score =  128 bits (321), Expect = 2e-34
 Identities = 90/281 (32%), Positives = 146/281 (51%), Gaps = 22/281 (7%)

Query: 66  SLLGVPLGHNSSFLQGPAFAPPRIR-EAIWCGSTNSATEEGKELKDPRVLTDVGDVPVQE 124
           + +GVPL   +S   G  F P +IR E++     N AT  G    D   + D+GDV +  
Sbjct: 42  AFIGVPLDIGTSLRSGTRFGPRQIRAESVMIRPYNMAT--GAAPFDSLSVADIGDVAINT 99

Query: 125 IRDCGVDDDRLMNVISESVKLVMEEEPLRPLVLGGDHSISYPVVRAVSEKLGGPVDILHL 184
                      + +I E+   ++E   + P+ LGGDH+I+ P++RA+ +K  G + ++H+
Sbjct: 100 FNLLDA-----VRIIEEAYDEIVEHNVI-PMTLGGDHTITLPILRALHKK-HGKIGLVHI 152

Query: 185 DAHPDIYDCFEGNKYSHASSFARIMEGGY--ARRLLQVGIRSINQEG------REQGKRF 236
           DAH D+ D   G K +H ++F R +E G     R++Q+G+R+           R QG  F
Sbjct: 153 DAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDRVVQIGLRAQGYTADDFNWSRRQG--F 210

Query: 237 GVEQYEMRTFSKDRPMLENLKLGEGVKGVYISIDVDCLDPAFAPGVSHIEPGGLSFRDVL 296
            V Q E        P++  ++   G   VY+S D+D +DPA+APG    E GGL+    +
Sbjct: 211 RVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDPAWAPGTGTPEIGGLTTIQAM 270

Query: 297 NILHNLQA-DVVGADVVEFNPQRDTVDGMTAMVAAKLVREL 336
            I+      D++G D+VE +P  DT  G T+++ A L+ E+
Sbjct: 271 EIIRGCHGLDLIGCDLVEVSPPYDTT-GNTSLLGANLLFEM 310


Lambda     K      H
   0.318    0.137    0.392 

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: 303
Number of extensions: 19
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 342
Length of database: 320
Length adjustment: 28
Effective length of query: 314
Effective length of database: 292
Effective search space:    91688
Effective search space used:    91688
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: 49 (23.5 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