GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aguA in Pseudomonas fluorescens FW300-N1B4

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate Pf1N1B4_4328 Agmatine deiminase (EC 3.5.3.12)

Query= BRENDA::O86509
         (339 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4328 Agmatine deiminase
           (EC 3.5.3.12)
          Length = 374

 Score =  234 bits (597), Expect = 3e-66
 Identities = 138/344 (40%), Positives = 193/344 (56%), Gaps = 18/344 (5%)

Query: 3   FRMPPEWAPHERTWMAWPGPNATFTDAEELAGARAAWASVARAVRRFEPVTMVHGPGQAA 62
           +RMP E   H R ++A+    A + D       + A   +AR +  +EPVT+     +  
Sbjct: 40  WRMPDEGDKHRRAFVAFGAQEAIWEDFTP--DVQEAIGLIARTIAHYEPVTVFCRSNERG 97

Query: 63  TARELLGP-DVDLVERELDDAWMRDIGPTFVTDGRGGLAAVDWVFNGWGAQDWARWEHDA 121
            A E  G  ++  V  ELDD WMRDIG  FV DG GGL AVD+ FNGWG +   ++  DA
Sbjct: 98  LAEEHCGTTNITYVTTELDDVWMRDIGANFVIDGAGGLGAVDFNFNGWGNKQ--QYSKDA 155

Query: 122 EIARHVADLAAAPVLSSPLVNEGGAIHVDGEGTVLLTDTVQLGSGRNPGWSREEVEAEIH 181
           ++A  VAD   A  + S LV EGG I VDG GT ++T++  + S RNP WS+ EVE E+ 
Sbjct: 156 QVAALVADTVDADHIRSELVGEGGGIEVDGHGTGIMTESSWINSNRNPDWSKAEVEQELK 215

Query: 182 AKLGTTTAIWLPHGLAGDYGRYGTQGHVDIVAAFARPGTVVVHSQRDPRHPDHERSQLYL 241
           A+LG    IWLP    G  G+  T  HVD  A F +PG V+ +   DP   D + +  +L
Sbjct: 216 ARLGLRKIIWLP----GIKGKDITDAHVDFYARFVKPGVVIANLDNDPESYDRKVTLAHL 271

Query: 242 EILRGRTDARGRRLEVVEVPAPTVLKDEEGEWA----DYS--YINHYVCNGGVVLCAFGD 295
           EIL+  TDA GR+L+V  V  P  L   + +++    D++  YIN++V NG ++   FGD
Sbjct: 272 EILKQATDADGRKLQVHTVSPP--LNPRKSKFSRNNPDFAAGYINYFVINGAIIAPEFGD 329

Query: 296 -PNDELAAGIFRRLFPERTVTLVDARTIFAGGGGIHCITQQQPR 338
              D  A  +   L+P+R V  ++   I AGGGGIHC+T  QP+
Sbjct: 330 KAADTRAFDLLSELYPDREVVQLNIDAIAAGGGGIHCVTSHQPQ 373


Lambda     K      H
   0.319    0.137    0.443 

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: 410
Number of extensions: 26
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: 339
Length of database: 374
Length adjustment: 29
Effective length of query: 310
Effective length of database: 345
Effective search space:   106950
Effective search space used:   106950
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: 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 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, 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