GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Pseudomonas putida KT2440

Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate PP_3205 PP_3205 Fumarylacetoacetate hydrolase family protein

Query= reanno::psRCH2:GFF3447
         (327 letters)



>FitnessBrowser__Putida:PP_3205
          Length = 330

 Score =  342 bits (878), Expect = 6e-99
 Identities = 176/327 (53%), Positives = 226/327 (69%), Gaps = 2/327 (0%)

Query: 1   MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59
           MKLAT + G RDG L+VV+RDL  AV    IA +LQ AL++W   + +L+A+YQ+LND  
Sbjct: 1   MKLATFDDGSRDGRLLVVARDLGHAVDASDIATSLQVALENWPQVEARLQALYQQLNDDA 60

Query: 60  EEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADA 119
             GAFA D     +PLPRA  W DGS +++H  L++KA   +  E   H PL+YQG +D 
Sbjct: 61  VAGAFALDLARLAAPLPRASQWLDGSCFLSHGALMQKAFNLDPIEGVEHTPLIYQGASDD 120

Query: 120 FIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPG 179
           F+ P + I L  EA GID EGE AV+ DDVPMG    +A  H++L++ +NDVSLR L P 
Sbjct: 121 FLGPLADIPLPSEAHGIDFEGEFAVLLDDVPMGCPAEQALQHVRLILQLNDVSLRALAPR 180

Query: 180 ELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTF 239
           E+  GFGF Q+KP+SSF+PVAVTPDELGE WRDG+VH PL  H NGE FG P  G  M F
Sbjct: 181 EMKTGFGFLQAKPASSFAPVAVTPDELGEAWRDGRVHLPLHVHWNGEWFGHPHGGA-MHF 239

Query: 240 NFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSAGSSCLAEKRMLEVVEHGEAKTPFLKFG 299
            F  L+AHAA TR L AGT++GSGTVSN +RS GS+C+AE+R +E +  G  +T F++FG
Sbjct: 240 GFHQLIAHAALTRRLSAGTLLGSGTVSNAERSVGSACIAERRAIETIACGAPRTAFMRFG 299

Query: 300 DRVRIEMFDAAGQSIFGAIDQQVERYG 326
           DRVR+E     G+ +FGAIDQ+V R G
Sbjct: 300 DRVRMEARGPEGEVLFGAIDQRVVRGG 326


Lambda     K      H
   0.318    0.135    0.411 

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: 383
Number of extensions: 13
Number of successful extensions: 2
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: 327
Length of database: 330
Length adjustment: 28
Effective length of query: 299
Effective length of database: 302
Effective search space:    90298
Effective search space used:    90298
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