GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Phaeobacter inhibens BS107

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__Phaeo:GFF2323
          Length = 396

 Score =  354 bits (908), Expect = e-102
 Identities = 186/384 (48%), Positives = 256/384 (66%), Gaps = 3/384 (0%)

Query: 21  TLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGN-VYSRYTNPTVRTFE 79
           T  V  G RR+   E  EA++ T  +V+ TA  A ARF    P   +Y+RY NPTV  FE
Sbjct: 9   TKLVHGGTRRSQYNEVSEAIYLTQGFVYDTAEQAEARFIETGPDEFIYARYGNPTVAMFE 68

Query: 80  ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139
           ERIAALEGAE A ATASGM+A+   + S+  +GDHV+ ++++FGS + + +    R+G++
Sbjct: 69  ERIAALEGAEDAFATASGMAAVNGALTSILKAGDHVVSAKALFGSCLYILENILTRYGVE 128

Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199
           V +   +DL AW AA +P+TK  F ES SNP  E++DIAA+AE+AHA GA + VDN F T
Sbjct: 129 VTFVDGTDLDAWRAALRPDTKAVFFESMSNPTLEVIDIAAVAELAHAVGATVVVDNVFST 188

Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVV-GFLRTAGPTLSPFNA 258
           P     ++ GADVVI+SATK+IDGQGR +GGV+ G  + ++  V  +++  G +LSPFNA
Sbjct: 189 PVFSNAIEQGADVVIYSATKHIDGQGRVLGGVILGTRDFIRGTVEPYMKHTGGSLSPFNA 248

Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSG-FG 317
           W  LKGLET+ +R+ A + +AL LA+ L   P + R+ Y GL  H QH L +RQ  G  G
Sbjct: 249 WTLLKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDHAQHALVQRQLGGKGG 308

Query: 318 AVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGD 377
            V+S D+KGG+DAA+RF++A  +  I+ NLGD K+   HPATT+H RLS E ++  GI  
Sbjct: 309 TVLSLDLKGGKDAAFRFLNALTIPVISNNLGDAKSIATHPATTTHQRLSEELKSELGITP 368

Query: 378 SLIRVAVGLEDLDDLKADMARGLA 401
            L+R +VGLED  DL AD+ + LA
Sbjct: 369 GLVRFSVGLEDAGDLIADLTQALA 392


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: 364
Number of extensions: 9
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: 396
Length adjustment: 31
Effective length of query: 372
Effective length of database: 365
Effective search space:   135780
Effective search space used:   135780
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