GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Shewanella sp. ANA-3

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 7026472 Shewana3_3614 cystathionine gamma-synthase (RefSeq)

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__ANA3:7026472
          Length = 393

 Score =  258 bits (659), Expect = 2e-73
 Identities = 154/399 (38%), Positives = 231/399 (57%), Gaps = 14/399 (3%)

Query: 7   AGRLDSDLEGAAFDTLAVRAG-QRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGN 65
           AG+L ++ + A   TLAVR G +  T  G     ++ +++Y F    +            
Sbjct: 3   AGKLVTERQLA---TLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFD------- 52

Query: 66  VYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGST 125
            YSR  NPT     + +A LE     V T +GM+AI  LV +L    D ++V    +G +
Sbjct: 53  -YSRSGNPTRSILGDALAKLEKGATGVVTCTGMAAI-TLVTTLLGPDDLLVVPHDCYGGS 110

Query: 126 ISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAH 185
             LF    K+   ++     +D  A E A     K+ ++E+PSNPL  +VDI A+A+ +H
Sbjct: 111 YRLFTNLAKKGQFKLLVVDQTDAQALEQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASH 170

Query: 186 AKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGF 245
           A GAL+ VDN F +P LQQPL LGAD+VIHS TKYI+G    +GG V  +  Q+ E + +
Sbjct: 171 AVGALVVVDNTFLSPILQQPLLLGADIVIHSTTKYINGHSDVVGGAVIAKDPQLGETLHW 230

Query: 246 L-RTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHP 304
              T G T S F+++  L+GL TL +R++ H ++A  + + L   P + +VYY GL  HP
Sbjct: 231 WSNTLGLTGSAFDSYQTLRGLRTLAVRIREHQSNAQRIVDVLTSSPVVSKVYYPGLADHP 290

Query: 305 QHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGR 364
            H +A +QQ GFGA++SF++KGG      F+DA  + S+  +LG  ++ +A PAT +H  
Sbjct: 291 GHAIAAKQQKGFGAMLSFELKGGEAEVVAFLDALSLFSVAESLGGVESLVAVPATMTHRA 350

Query: 365 LSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403
           + P+ R  AGI D+L+R++VG+ED DDL AD+  GLAA+
Sbjct: 351 MEPQARFEAGIKDTLLRLSVGIEDADDLVADIQAGLAAV 389


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: 349
Number of extensions: 17
Number of successful extensions: 3
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: 393
Length adjustment: 31
Effective length of query: 372
Effective length of database: 362
Effective search space:   134664
Effective search space used:   134664
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 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