GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocF in Pseudomonas putida KT2440

Align arginase (EC 3.5.3.1) (characterized)
to candidate PP_2196 PP_2196 agmatinase

Query= metacyc::MONOMER-14988
         (338 letters)



>lcl|FitnessBrowser__Putida:PP_2196 PP_2196 agmatinase
          Length = 311

 Score =  100 bits (248), Expect = 6e-26
 Identities = 78/271 (28%), Positives = 121/271 (44%), Gaps = 15/271 (5%)

Query: 65  GIPLGHNSSFLQGPAFAPPLIREAIWCGSTNSTTEEGKILDDQRVLTDVGDLPVQELRDT 124
           G+P    +S   G  F P  IR A    +            D   + D GD P       
Sbjct: 39  GVPFDTATSNRPGARFGPRAIRAASVQQAWARHWPWAFDPFDHLAVIDYGDCPFDSGTPQ 98

Query: 125 GIDDDRLMSTVSESVKLVMDENPLRPLVLGGDHSISYPVVRAVSEKLGGPVDILHLDAHP 184
            + D     ++    + ++       L LGGDH ISYP+++A + +  GP+ ++H DAH 
Sbjct: 99  SVPD-----SIEAHAEHILQAG-CAMLTLGGDHFISYPLLKAHARR-HGPLALIHFDAHS 151

Query: 185 DIYDAFEGNKYSHASSFARIMEGGYA--RRLLQVGIRSINLEGREQGKRFGVEQYEMRTF 242
           D +    G +  H + F      G       +Q+G+R+ N    +  + F +        
Sbjct: 152 DTWPDEAGKRIDHGTMFWHAAREGLVDPAHSVQIGLRTTN----DDSQGFAILDARQVHR 207

Query: 243 SRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHFESGGLSFRDVLNILHNLQG-D 301
                 +  ++   G + VY++ D+DCLDPA+APG      GGLS    L IL  L+G +
Sbjct: 208 QGTEAVIAAIRQRVGERPVYLTFDIDCLDPAYAPGTGTPVCGGLSTVQALEILGGLRGIN 267

Query: 302 IVGADVVEYNPQRDTADGMTAMVAAKLVREL 332
           +VG D+VE  P  D AD +TA+  A L  E+
Sbjct: 268 LVGMDLVEVAPAYDHAD-ITALAGATLAMEM 297


Lambda     K      H
   0.317    0.137    0.387 

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: 263
Number of extensions: 15
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: 338
Length of database: 311
Length adjustment: 28
Effective length of query: 310
Effective length of database: 283
Effective search space:    87730
Effective search space used:    87730
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 (21.6 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 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