GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4328
          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 (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