GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Neptunomonas antarctica S3-22

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_054341061.1 Nant_RS07655 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_001305295.1:WP_054341061.1
          Length = 393

 Score =  313 bits (802), Expect = 6e-90
 Identities = 175/404 (43%), Positives = 253/404 (62%), Gaps = 16/404 (3%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M E +I+ A RT +G + G+LA V+A DLGA  LK L+ +  ++D + +D+VI G    A
Sbjct: 1   MREVVIVAAGRTAVGTFNGSLAGVKASDLGATVLKGLLEQ-TKIDPAQIDEVILGQVLAA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR A + AG+P      TLN++CGSGL A+  AA+A+RCG+A +++AGG E+M
Sbjct: 60  G-CGQNPARQALINAGIPQEASAFTLNKVCGSGLKAIQLAAQAIRCGDADMIIAGGQENM 118

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQG----FGIDSMPETAENVAAQFNI 176
           S++P V+  S                W+ V+ ++  G    F    M  T EN+  ++  
Sbjct: 119 SQSPHVLPNSRNGVRMG--------DWKMVDTMITDGLWDAFNNYHMGITTENIVEKYGF 170

Query: 177 SRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLA 236
           +R +QDAFA  SQ+KA  A+ +GR   EI+ V I QRKG   + + DE PR   T E LA
Sbjct: 171 TREEQDAFASASQNKAEVAVTSGRFKDEIIPVVIPQRKGDPVVFDTDEQPRFGCTPEALA 230

Query: 237 KLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMG 296
           KL   F++ G+VTAGN+S +NDGA A++L S+E A   GL   AR+   A+AGV+P IMG
Sbjct: 231 KLRPAFKKDGTVTAGNSSTLNDGAAAVILCSAEKAAELGLPVLARIKAYASAGVDPAIMG 290

Query: 297 IGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALG 356
            GP+ AT+K L+  G  + D++++E NEAFAAQ ++V ++LG   + + VN NGGAIA+G
Sbjct: 291 TGPICATQKALKKAGWTVDDLELVEANEAFAAQAMSVNKDLGW--NSKIVNVNGGAIAMG 348

Query: 357 HPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           HP+G SG R+  + +HE+ +R  +  L T+CIG G G AL IER
Sbjct: 349 HPIGASGCRIFVSLIHEMIKRDAKKGLATLCIGGGMGTALAIER 392


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: 398
Number of extensions: 16
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
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