GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Shewanella oneidensis MR-1

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 201209 SO2052 hypothetical oxidoreductase (NCBI ptt file)

Query= reanno::pseudo6_N2E2:Pf6N2E2_80
         (394 letters)



>lcl|FitnessBrowser__MR1:201209 SO2052 hypothetical oxidoreductase
           (NCBI ptt file)
          Length = 429

 Score =  296 bits (757), Expect = 1e-84
 Identities = 156/397 (39%), Positives = 234/397 (58%), Gaps = 10/397 (2%)

Query: 1   VIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGASGRNGGQIVNSYSRDIDV---IERSV 57
           +IG G+TG+++A+ L E G+KV +LEA K+ +GA+GRNGGQ+  S S D  +   + R +
Sbjct: 33  IIGGGFTGVATAVELSEKGYKVALLEANKIAWGATGRNGGQVTGSLSGDAAMTKQLRRHL 92

Query: 58  GPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVFAALTAKQMGHLESQKRLWERFG 117
           G      + N+ + G  II+ RVAKY I CDLK G +    TA   GH++  +++++   
Sbjct: 93  GQDAEDYVWNLRWRGHDIIKNRVAKYGIDCDLKFGHI---QTAYHPGHMQELQQMFDEAN 149

Query: 118 HTQL----ELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNLALGEAAAVESLGGVIYEQ 173
              +     L+  + +   +A   Y GG+++    H+H +NL LGEA A  SLG  I+E 
Sbjct: 150 RRGMGEFMTLVPAQEMSAYLASPLYHGGLVNRRNMHLHSVNLCLGEARAAASLGAQIFEH 209

Query: 174 SPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVIATEPLGD 233
           S  + I++     V TP+G V+A  +++AGNAY     P+L     P      AT  L +
Sbjct: 210 SQVLDIQQAELATVVTPKGTVKANSVLIAGNAYHKLGRPKLRGMLFPASLGNCATAKLPE 269

Query: 234 ELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFP 293
           ELA  L PQ+  V DC ++LDYYRLT D RL+FGGG  Y  RDP N+ A +RP + + FP
Sbjct: 270 ELAKQLNPQNLAVYDCRFVLDYYRLTADNRLMFGGGTNYSGRDPKNVAAELRPAIERTFP 329

Query: 294 QLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQ 353
           QLK V I++AW G   + ++R+PQ+G++  NI+Y QG SGHGV  +H+  +++ +A+ GQ
Sbjct: 330 QLKGVDIEFAWAGMAGIVINRIPQLGKISPNIFYCQGYSGHGVATSHIMAEIMGQAIDGQ 389

Query: 354 AERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 390
            + FD FA + H   P  +       A+G  YY LR+
Sbjct: 390 MQEFDLFAAMRHIRIPLNEWFGNQALALGMLYYTLRE 426


Lambda     K      H
   0.321    0.140    0.423 

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: 533
Number of extensions: 24
Number of successful extensions: 3
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: 394
Length of database: 429
Length adjustment: 31
Effective length of query: 363
Effective length of database: 398
Effective search space:   144474
Effective search space used:   144474
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: 50 (23.9 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 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