GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Pseudomonas simiae WCS417

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__WCS417:GFF2301
          Length = 411

 Score =  295 bits (756), Expect = 1e-84
 Identities = 160/389 (41%), Positives = 241/389 (61%), Gaps = 8/389 (2%)

Query: 19  FDTLAVRAGQRRTPEGEHGEA---LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTV 75
           F T A+  G    P+  HG     ++ ++++ F TA   AA FAGE  G+ Y+R +NPT+
Sbjct: 10  FSTRAIHHGY--DPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTRISNPTL 67

Query: 76  RTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKR 135
              E R+A LE  + AVA +SGM AI A   +L   GD V+VS++++G T +L       
Sbjct: 68  ALLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALLHHGIGE 127

Query: 136 FGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAK-GALLAVD 194
           FGI+V +  L+DL A +AA  P T++ + E+P+NP   LVDIAA+A +AH +    L VD
Sbjct: 128 FGIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQPNVTLVVD 187

Query: 195 NCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGE--QMKEVVGFLRTAGPT 252
           N +CTP LQ+PL+LGADVV+HSATKY+ G G    G+        Q   + G     G  
Sbjct: 188 NTYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAVSNQALAQRIRLQGLKDLTGAV 247

Query: 253 LSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQ 312
           +SP +A L ++GL+TL +RM  H ++A A+AE L+  P ++ V Y GL S PQ+ELA +Q
Sbjct: 248 MSPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSFPQYELATQQ 307

Query: 313 QSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372
               G +++F++KGG +   RF++A ++ +   +LGD ++   HPA+ +H   +P++RA 
Sbjct: 308 MKMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHSTYTPQERAA 367

Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLA 401
            GI + L+R++VGLED+ DL AD+ + LA
Sbjct: 368 HGISEGLVRLSVGLEDVADLLADVQQALA 396


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: 396
Number of extensions: 13
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: 411
Length adjustment: 31
Effective length of query: 372
Effective length of database: 380
Effective search space:   141360
Effective search space used:   141360
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.

Links

Downloads

Related tools

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