GapMind for Amino acid biosynthesis

 

Alignments for a candidate for SST in Echinicola vietnamensis KMM 6221, DSM 17526

Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate Echvi_3285 Echvi_3285 homoserine O-acetyltransferase

Query= SwissProt::S2KHP1
         (367 letters)



>FitnessBrowser__Cola:Echvi_3285
          Length = 351

 Score =  182 bits (461), Expect = 2e-50
 Identities = 115/344 (33%), Positives = 176/344 (51%), Gaps = 26/344 (7%)

Query: 19  GGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMADPSPGWWEYMIGPGKPID 78
           G  LP   I+Y T G L  + DN + +   L+  A+           WW  ++G  K  D
Sbjct: 28  GESLPGFEISYTTQGHLTPKKDNVIWILHALTGDANVHE--------WWSGLVGEDKFFD 79

Query: 79  TERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGACRALGIDHV 138
             ++F++  N LGSC+GST P S NP TG+PY  DFP LS  D+  A     + LGI  +
Sbjct: 80  PTKYFIVCANLLGSCYGSTQPLSDNPKTGKPYYYDFPNLSTRDMAKAFDRLRQHLGIQQI 139

Query: 139 HTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVRADPAWAGG 198
            T+ G SLGG  AL ++       +  I +++ A  +P+TI     QR A+ +D  W  G
Sbjct: 140 DTIIGGSLGGQVALEWSYNLQEQVKKTIIVASNAKTSPWTIGFNEAQRMAIESDSTW--G 197

Query: 199 NYAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPFAMAFQVQSYMEA 258
             +P  G K G+  AR +G+L+YR  ++       E  E +D         F+V SY+  
Sbjct: 198 QNSPDAG-KKGLEAARAIGMLSYRH-QDIFHASQAETEEKTDH--------FRVSSYLRY 247

Query: 259 NARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVAGVTTDWLFPLW 318
             +K ++RF+A  Y  L++AMD  D+   G G    A+  I AK  L  G+ TD LF   
Sbjct: 248 QGQKLSNRFNALSYWVLTKAMDSHDLG-RGRGGTAKALSAIKAK-VLSIGINTDLLFTKE 305

Query: 319 QQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEF 362
           + + +++ + +     +Y E+ SI GHDAFLV++E+   ++  F
Sbjct: 306 ESQFISKNVPNG----TYREISSIYGHDAFLVENEQLNYILTSF 345


Lambda     K      H
   0.320    0.135    0.414 

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: 291
Number of extensions: 22
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: 367
Length of database: 351
Length adjustment: 29
Effective length of query: 338
Effective length of database: 322
Effective search space:   108836
Effective search space used:   108836
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: 49 (23.5 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