GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguA in Pseudomonas fluorescens GW456-L13

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate PfGW456L13_2706 Agmatine deiminase (EC 3.5.3.12)

Query= BRENDA::Q9I6J9
         (368 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2706
          Length = 374

 Score =  212 bits (539), Expect = 2e-59
 Identities = 122/350 (34%), Positives = 177/350 (50%), Gaps = 20/350 (5%)

Query: 15  MPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPVTVCASAGQYENARA 74
           MP E + H++ ++ +  +   W +     Q A   +A++IA  EPVTV     +   A  
Sbjct: 42  MPDEGDKHQRAFIAFGAQAAIWEDFTPHVQDALGRIARSIAEHEPVTVFCRQSERRLAEV 101

Query: 75  RLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGGFEGGLYFPWQRDDQ 134
           +    N   V    DD W+RD G  FV+D  G +  VD+ FN WG  +         DD 
Sbjct: 102 KCGSHNTTFVITELDDIWMRDIGANFVVDGSGGLAAVDFNFNGWGNKQQ------HADDA 155

Query: 135 VARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHLSQAEIERTLR 194
               ++    +A Y+  + V EGG I VDG GT I TE   +N NRNP  S+AE+E  L+
Sbjct: 156 QLAALVAENAKADYQRSELVGEGGGIEVDGHGTGIMTESSWINRNRNPDWSKAEVEAELK 215

Query: 195 DYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYLRCQAALRVLE 254
           + L +  IIWLP     D TD HVD +  + +PG V+    +D +  +Y   +A L++LE
Sbjct: 216 ERLGLRKIIWLPGIKGKDITDAHVDFYARFVKPGVVIANLDNDPESYDYKVTRAHLQILE 275

Query: 255 ESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGSQPRDPSIRLAGSYVNFLIVNGGI 314
            + DA GRKL VH +  P     ++   D  D   G             Y+N+ ++NG I
Sbjct: 276 NATDADGRKLQVHTVSPPLNPRNSRFSNDNPDFAAG-------------YINYFVINGAI 322

Query: 315 IAPSF-DDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQQQP 363
           IAP F D+  DA+A  +L  ++P+ EVV +    I  GGG IHC+T  QP
Sbjct: 323 IAPQFGDEEADAKAFDLLSELYPDREVVQLDIDAISAGGGGIHCVTSHQP 372


Lambda     K      H
   0.319    0.138    0.439 

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: 452
Number of extensions: 23
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: 368
Length of database: 374
Length adjustment: 30
Effective length of query: 338
Effective length of database: 344
Effective search space:   116272
Effective search space used:   116272
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 (21.7 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