GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:201209
          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.

Links

Downloads

Related tools

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