GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Herbaspirillum seropedicae SmR1

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate HSERO_RS05840 HSERO_RS05840 FAD-dependent oxidoreductase

Query= reanno::pseudo5_N2C3_1:AO356_21495
         (427 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05840 HSERO_RS05840
           FAD-dependent oxidoreductase
          Length = 433

 Score =  197 bits (502), Expect = 4e-55
 Identities = 138/424 (32%), Positives = 201/424 (47%), Gaps = 9/424 (2%)

Query: 2   ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61
           +N  +P S +AA+A      P LQ     DV ++GAGYTGLS+AL L + G  V VL+A 
Sbjct: 5   SNPAFPPSLWAATAGEFSGAPPLQASARYDVAIVGAGYTGLSTALHLAQAGVSVCVLDAH 64

Query: 62  KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121
             G+GASGRNGGQ++     D D +    G   A  L          + + +A++ I+C+
Sbjct: 65  APGWGASGRNGGQVIPGLKYDPDQLRVMFGSAVADPLIAAIGSAADTVFDLIARHGIECE 124

Query: 122 LKDGG-VFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180
            +  G +    + K M  LE++ R W   G    +L+D   +   +    YVGG  D   
Sbjct: 125 AQRAGWIQPTHSPKMMRALEARARQWMAEG-APAQLMDGAEVTRRIGTGAYVGGWKDERA 183

Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASP-VVHTPQGK----VRAKFIIVA 235
           G +HPL    G A A + LG VI+  +   R+ER      +H P G+    + A+ +++A
Sbjct: 184 GSLHPLKYCRGLAQAAQRLGVVIHGDTRVTRLERRQGGWRLHGPSGEQGPHIDAERVVLA 243

Query: 236 GNAYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDK 295
            N Y  +L P L    +   + ++AT PL   L  S+LP      D   LL YYR     
Sbjct: 244 TNGYTDDLWPHLRQSVIAANSFIVATRPLPPALGASILPGGEVTSDSRRLLLYYRRDAQG 303

Query: 296 RLIFGGGVVYG-ARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRL 354
           RL+ GG   +G  + PA+   + R   L  FPQL  V+ +Y W+G   +T   LP V   
Sbjct: 304 RLLMGGRGPFGEPQGPADFAHLERSVAL-LFPQLAGVEYEYRWSGRVAITRDFLPHVHEP 362

Query: 355 GDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAM 414
              +  + G +G G+    + G+ LA+ L G A     F      P P   L R   AA 
Sbjct: 363 APGLSIALGYNGRGIAMATMMGQRLAQRLIGPAGTAFPFPVSTIAPIPLHGLQRFYIAAG 422

Query: 415 GAWY 418
            AWY
Sbjct: 423 VAWY 426


Lambda     K      H
   0.320    0.139    0.421 

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: 512
Number of extensions: 26
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: 427
Length of database: 433
Length adjustment: 32
Effective length of query: 395
Effective length of database: 401
Effective search space:   158395
Effective search space used:   158395
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: 51 (24.3 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