GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Neptunomonas antarctica S3-22

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_054339946.1 Nant_RS01890 acetyl-CoA C-acyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_001305295.1:WP_054339946.1
          Length = 394

 Score =  307 bits (787), Expect = 3e-88
 Identities = 178/394 (45%), Positives = 242/394 (61%), Gaps = 11/394 (2%)

Query: 9   GIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNRNVA 68
           G+RT IG +GG+L +    +LAA  + E + R+  ++       ++G        +  + 
Sbjct: 11  GVRTAIGGFGGSLKTKTPCELAAAVVEEAVKRSG-VEPAAFGHSVIGNVIHTERRDMYIG 69

Query: 69  RMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPFVMG 128
           R+A +  GLP    G T+NRLCGSGL A+  AA+ I+ G     +AGG E MSR+ + + 
Sbjct: 70  RVAAVNGGLPHETPGLTVNRLCGSGLQAIITAAQQIELGQCSAAVAGGAEVMSRSQYWIP 129

Query: 129 KAASAFSR-QAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQDSFALR 187
            A        AE+ D  +G       +   F    M  TAENVAE  KISREDQD+ AL 
Sbjct: 130 SARFGQRMGDAEIVDAMVG------ALTCPFDDTHMGITAENVAEKWKISREDQDALALL 183

Query: 188 SQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRANGV 247
           S QR   A +SG   ++I+P+ LK++KG  T    DEH R   TLE +  L+  F+ +G 
Sbjct: 184 SHQRAEAATTSGRFKDQILPIELKSRKGS-TFFDTDEHTRKGCTLEDMTKLRPAFKRDGS 242

Query: 248 ITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPATRRVL 307
           +TAGNASG+ND AAA+ + S   AA +GL P AR+   A AGVEP+ MG+GP+PA R++L
Sbjct: 243 VTAGNASGLNDAAAAVTLMSSDEAAKRGLKPMARLAGYAFAGVEPKYMGIGPIPAVRKLL 302

Query: 308 ERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGARLA 367
           + AGLSI D+DV E+NEAFAAQAL V R+L LP D   VN NG  ++LGHP+G +GA + 
Sbjct: 303 DNAGLSISDIDVWEVNEAFAAQALAVARDLDLPAD--KVNVNGSGVSLGHPIGATGAIIT 360

Query: 368 LAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           + A +EL R  GRYA+ TMCIG GQGIA +LER+
Sbjct: 361 VKALYELQRVEGRYAVVTMCIGGGQGIAALLERI 394


Lambda     K      H
   0.319    0.135    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: 413
Number of extensions: 20
Number of successful extensions: 5
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: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
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 24 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