GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Nocardiopsis lucentensis DSM 44048

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_017597122.1 D471_RS0102240 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P55218
         (403 letters)



>NCBI__GCF_000341125.1:WP_017597122.1
          Length = 390

 Score =  277 bits (708), Expect = 4e-79
 Identities = 146/366 (39%), Positives = 215/366 (58%), Gaps = 2/366 (0%)

Query: 37  GEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATAS 96
           G  ++   ++ F      AA F G     VY+RY NPTV   E+ +A LEG   A+A+ S
Sbjct: 24  GVPIYQAHTFAFPDTETMAASFQGAGSPFVYARYGNPTVAALEDAVADLEGGAGAIASGS 83

Query: 97  GMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACK 156
           GM AI A + +L  +G HV+    ++G T +L     +R+G++V      D AA +AA +
Sbjct: 84  GMGAITATLWALLGTGGHVVAQERLYGGTQALLTTLRERWGVEVTQVDAGDPAAVDAALR 143

Query: 157 PNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHS 216
           P+T++  +E+ +NP  ++ D+ AL  +A   G  + VDN F TP L +P++ GAD+V+HS
Sbjct: 144 PDTRVLVLETIANPTGQVADLPALTALARRHGTTVIVDNTFATPLLCRPIEHGADIVVHS 203

Query: 217 ATKYIDGQGRGMGGV-VAGRGEQMKEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAH 275
           ATKY+ G    +GGV V      +  V       G  + PF AWL  +GL TL +RM+ H
Sbjct: 204 ATKYMGGHSDTIGGVAVFADAGTLTRVRERTNEFGAVMEPFAAWLINRGLSTLGVRMRRH 263

Query: 276 SASALALAEWLERQPGIERVYYAGLPSHPQHELARR-QQSGFGAVVSFDVKGGRDAAWRF 334
            A+A  LA  L+R P + RV+YAGLP HP H  AR     GFG V++F++ GG +A   F
Sbjct: 264 CANAEELARRLDRHPAVTRVHYAGLPDHPGHATARELLDGGFGGVLAFELAGGLEAGRSF 323

Query: 335 IDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKA 394
            +  R+  +  +LGD +T + HPA+TSH  L  E  ARAG+ + LIR++ G+ED++DL A
Sbjct: 324 AERVRLAVLAPSLGDVRTLVMHPASTSHRMLDAEGLARAGVSEGLIRLSAGIEDVEDLWA 383

Query: 395 DMARGL 400
           D+ R L
Sbjct: 384 DLERAL 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: 406
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: 390
Length adjustment: 31
Effective length of query: 372
Effective length of database: 359
Effective search space:   133548
Effective search space used:   133548
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