GapMind for Amino acid biosynthesis

 

Alignments for a candidate for SST in Caulobacter crescentus NA1000

Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate CCNA_00559 CCNA_00559 homoserine O-acetyltransferase

Query= SwissProt::A0A0I9RJ56
         (370 letters)



>FitnessBrowser__Caulo:CCNA_00559
          Length = 382

 Score =  248 bits (633), Expect = 2e-70
 Identities = 142/353 (40%), Positives = 196/353 (55%), Gaps = 4/353 (1%)

Query: 17  PFPFKRGGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAAA-NDANPAAGWWEGMV 75
           P     GG + G  +AY+T+G L AD SNA+LI   L+ D H A+ +      GWW+ +V
Sbjct: 22  PLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGWWQRLV 81

Query: 76  GPGKAIDTDRWFVVCVNSLGSCRGSTGPASLNPATGQPYRLDFPELSIEDGARAAIEVVR 135
           GPGK +D  R F++C N +G C GSTGPAS+NPATG+ Y L FP ++I D  RA   +V 
Sbjct: 82  GPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQAMLVS 141

Query: 136 AQGIEQLACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALPFSIAIRSLQREAIRL 195
           A G+E L  VVG SMGGM      + +P    S V ++ +++    +IA   + R+AI  
Sbjct: 142 ALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGRQAIMA 201

Query: 196 DPRWNGGHY-DDDAYPESGMRMARKLGVITYRSALEWDGRFGRVRLDSDQTDDDPFGLEF 254
           DP W GG Y +    PE G+ +AR    ITY S      +FGR  L  D      F  +F
Sbjct: 202 DPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGR-ELQRDGLSWG-FDADF 259

Query: 255 QVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEYADGDVLAGLAKIRVEKALAIGAN 314
           QVESYL      FV  FD N YLY++R+MD+FD+A    G +     + R  +   +  +
Sbjct: 260 QVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCVLSFS 319

Query: 315 TDILFPVQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFERFCPAVRGFL 367
           +D L+P  + + +   L A GA A F  +ES +GHDAFL+D      A+ GFL
Sbjct: 320 SDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFL 372


Lambda     K      H
   0.322    0.138    0.432 

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: 402
Number of extensions: 19
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: 370
Length of database: 382
Length adjustment: 30
Effective length of query: 340
Effective length of database: 352
Effective search space:   119680
Effective search space used:   119680
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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