GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Methylocella silvestris BL2

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012592297.1 MSIL_RS16900 PLP-dependent transferase

Query= SwissProt::P55218
         (403 letters)



>NCBI__GCF_000021745.1:WP_012592297.1
          Length = 392

 Score =  216 bits (550), Expect = 9e-61
 Identities = 133/363 (36%), Positives = 195/363 (53%), Gaps = 8/363 (2%)

Query: 40  LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMS 99
           +F TSS+ F    D A  +AG     +YSR  NPTV  FE  +A L+GAE A A +SGM 
Sbjct: 33  IFQTSSFFFDNFDDMADVYAGRSRRLIYSRGDNPTVMEFERVMAELDGAEAARAFSSGMG 92

Query: 100 AILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNT 159
           AI A +++  S+GD ++  R+V+     LF+    +FG+ VDY   +D  A  AA  P  
Sbjct: 93  AIAATIIAFVSAGDRIVTVRNVYSDAYRLFELVLAKFGVTVDYLDGADAGA-IAAALPGA 151

Query: 160 KLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATK 219
           KL ++E+P++   EL DIA LA +A A+G +  +DN + TP  Q+P+  G D+VIH+A+K
Sbjct: 152 KLLYLETPTSLTFELQDIATLAALARAQGVVSVIDNSWATPQFQKPIAHGVDLVIHAASK 211

Query: 220 YIDGQGRGMGGVVAGRGEQMKEV-VGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSAS 278
           Y+ G    + GVV+G  E +  +  G     G  LSPF AWL L+GL TL +R+  H  S
Sbjct: 212 YLGGHSDTVAGVVSGSAEHVARINAGAYAYLGAKLSPFEAWLLLRGLATLELRLPRHMQS 271

Query: 279 ALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDAT 338
            L +A  L+  P +  V +     HP     +   SGF  + S +V    D    F +A 
Sbjct: 272 GLLIAGRLKAHPNVSLVRHPAYSDHP----GKATLSGFSGLFSIEVGENIDVR-TFANAL 326

Query: 339 RMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMAR 398
           ++  +  + G  ++ +  PA       +    AR G+   LIR+ VGLED + L  D+ R
Sbjct: 327 KLFRLGVSWGGPESLVV-PALAPLQLRTANCFARFGVSPRLIRLHVGLEDAEALWDDLER 385

Query: 399 GLA 401
            LA
Sbjct: 386 ALA 388


Lambda     K      H
   0.319    0.133    0.392 

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: 384
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: 403
Length of database: 392
Length adjustment: 31
Effective length of query: 372
Effective length of database: 361
Effective search space:   134292
Effective search space used:   134292
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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