GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Burkholderia phytofirmans PsJN

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate BPHYT_RS33835 BPHYT_RS33835 O-succinylhomoserine sulfhydrylase

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__BFirm:BPHYT_RS33835
          Length = 396

 Score =  451 bits (1159), Expect = e-131
 Identities = 221/389 (56%), Positives = 294/389 (75%), Gaps = 6/389 (1%)

Query: 19  FDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTF 78
           FDTLAVR+G  R+   EH EA+F TSS+VF +AADAA +F        YSR+TNPTV  F
Sbjct: 7   FDTLAVRSGTVRSDFNEHSEAIFLTSSFVFESAADAAEKFKNSEDNYTYSRFTNPTVSMF 66

Query: 79  EERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGI 138
           ++R+AALEG E  +ATASGM+AI+++VMS   +GDH++ S+++FGST+ +F + F +FGI
Sbjct: 67  QDRLAALEGGEACMATASGMAAIMSVVMSTLQAGDHLVSSQALFGSTLGMFSQIFSKFGI 126

Query: 139 QVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFC 198
              +   +DL AW+ A +P TK+FF+E+PSNPL E+ DI A+++IA+A  AL  VDNCFC
Sbjct: 127 TTTFVDPTDLDAWKNAVRPETKMFFLETPSNPLTEVADIEAISKIANASNALFVVDNCFC 186

Query: 199 TPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGE-QMKEVVGFLRTAGPTLSPFN 257
           +PALQQPLKLGADVV+HSATK++DGQGR +GG + G  +  M++V  F+R+AGPTLS FN
Sbjct: 187 SPALQQPLKLGADVVMHSATKFLDGQGRVLGGALVGSKQFIMEKVFPFVRSAGPTLSAFN 246

Query: 258 AWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFG 317
           AW+ LKG+ETL +R++  SA+AL +A WLE  P + RV+Y GL SHPQH LA RQQ   G
Sbjct: 247 AWVLLKGMETLSLRVEKQSANALEIARWLEAHPAVNRVFYPGLESHPQHALAMRQQKAGG 306

Query: 318 AVVSFDVKGG-----RDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372
           A++SF++KG      R  AWR ID T++ SIT NLGDT+TTI HPATT+HGR++PE RA 
Sbjct: 307 AILSFELKGDTPEQMRANAWRVIDNTKICSITGNLGDTRTTITHPATTTHGRVTPEARAA 366

Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLA 401
           AGI + LIR+AVGLE+  D++ D+ RGLA
Sbjct: 367 AGISEGLIRLAVGLENAGDIRGDLERGLA 395


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: 438
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: 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 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