GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Shewanella oneidensis MR-1

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate 202206 SO3089 fatty oxidation complex, beta subunit (NCBI ptt file)

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__MR1:202206
          Length = 436

 Score =  172 bits (437), Expect = 1e-47
 Identities = 132/425 (31%), Positives = 209/425 (49%), Gaps = 38/425 (8%)

Query: 6   IIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGEDNR 65
           I+  +RTP  + A A   + A D+G + +  L+ R  +LD   ++ ++YG   Q      
Sbjct: 17  IVAGLRTPFAKQATAFHGISALDMGKMVVNELLVRS-ELDPKLIEQLVYGQVVQMPAAP- 74

Query: 66  NVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSRAPF 125
           N+AR   L  G+ VS    ++ R C +   +  + A ++  G   + +AGG +S S  P 
Sbjct: 75  NIAREIVLGTGMDVSTDAYSVTRACATSFQSAVNVAESIMTGNIEIGIAGGADSSSVLPI 134

Query: 126 VMGKS----------EQAFGRSAEIFDTTIGWRFV----NKLMQQGFGIDSMPETAENVA 171
            + K            + FG+  +IF   +G + +      + +   G+ SM +TAE +A
Sbjct: 135 GVSKKLAHALVDLNKARTFGQKLQIF-RRLGIKDLLPVPPAVAEYSTGL-SMGQTAEQMA 192

Query: 172 AQFNISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTT 231
             +NISRADQDA A RS   A    A+G L  E++   +   K   + +E D + R ++ 
Sbjct: 193 KTYNISRADQDALAHRSHTLANETWASGHLRDEVMVAHVPPYK---QFIERDNNIRENSD 249

Query: 232 LEQLAKLGTPF-RQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGV 290
           L   AKL   F ++ GSVTA N++ + DGA A++L S   A+  G +    +   A   +
Sbjct: 250 LASYAKLRPAFDKKHGSVTAANSTPLTDGASAIILMSEGRAKALGYQPIGYIKSYAFTAI 309

Query: 291 EP-RIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVL--------------R 335
           +  + M +GP  AT   L+  G+ L D+ +IE++EAFAAQ LA +              R
Sbjct: 310 DVWQDMLMGPSYATPLALKRAGMELEDLTLIEMHEAFAAQTLANMQMFASKKFAEEKLGR 369

Query: 336 ELGLADDD-ERVNPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGI 394
              + D D  + N  GG++A GHP   +G RL+T    EL+ R G   L T C   G G 
Sbjct: 370 NRAIGDIDMSKFNVLGGSLAYGHPFAATGTRLITQVCRELKRRGGGTGLATACAAGGLGA 429

Query: 395 ALIIE 399
           A+I+E
Sbjct: 430 AMIVE 434


Lambda     K      H
   0.319    0.134    0.384 

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: 380
Number of extensions: 23
Number of successful extensions: 6
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: 401
Length of database: 436
Length adjustment: 32
Effective length of query: 369
Effective length of database: 404
Effective search space:   149076
Effective search space used:   149076
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:

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