Alignments for a candidate for metZ in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for metZ in Acidovorax sp. GW101-3H11

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Ac3H11_34 Methionine gamma-lyase (EC 4.4.1.11)

Query= SwissProt::P9WGB5
         (406 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_34
          Length = 434

 Score =  263 bits (672), Expect = 7e-75
 Identities = 152/368 (41%), Positives = 220/368 (59%), Gaps = 6/368 (1%)

Query: 40  MYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPTVSVFEERLRLIEGAPAAFATASGMA 99
           ++ ++ Y +   A   + FAG+   Y Y+R  NPT+++ E RL  +E    A    SGM 
Sbjct: 35  IHTSATYAFPDVAYGARCFAGQEPGYFYTRIANPTLALLEGRLAALEEGAGAVVFGSGMG 94

Query: 100 AVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTVFVDGDDLSQWERALSVPT 159
           A+  +L ++L  GD ++A  +L+G  F      L R+GV    VD  D ++   AL+  T
Sbjct: 95  AITATLWSMLEPGDEILADLTLYGCTFSFLHHGLGRFGVTVRHVDMTDPARVAEALTAKT 154

Query: 160 QAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFATPLLQQGFPLGVDVVVYSGTK 219
           + ++ ETP+NP   LVDIAAV+ LAHA GAKVV+DN + TP LQQ   LG DV V+S TK
Sbjct: 155 RVLYLETPANPNMRLVDIAAVSALAHAQGAKVVVDNTYCTPYLQQPLLLGADVSVHSMTK 214

Query: 220 HIDGQGRV-LGGAILGDREYIDG-PVQKLMRHTGPAMSAFNAWVLLKGLETLAIRVQHSN 277
           ++ G G +  G A+  D E      +  L   TG  MSA +A ++++GL+TLA+R+    
Sbjct: 215 YLGGHGDLTAGAAVFADAELAQRVRLYGLKDMTGAVMSAQDAHLVMRGLKTLALRMDRHC 274

Query: 278 ASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGTVVTFALDCPEDVAKQRAF 337
            SAQ++AEF+  HP+   V YP LPS  Q+ LAK+QM   G ++ F L        Q   
Sbjct: 275 QSAQKVAEFIAAHPAAAAVHYPGLPSFAQHALAKQQMRQMGGMIAFEL----RGGLQAGV 330

Query: 338 EVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIGLGDGVVRISVGLEDTDDL 397
             +D ++L+  + +LGDA++L  HPA+ TH    PE RAA G+ +G+VR+SVGLED DDL
Sbjct: 331 RFMDALQLVTRAVSLGDAETLAQHPASMTHSTYTPEQRAAHGIAEGLVRLSVGLEDLDDL 390

Query: 398 IADIDRAL 405
           +ADI +AL
Sbjct: 391 LADIGQAL 398


Lambda     K      H
   0.319    0.135    0.395 

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: 480
Number of extensions: 16
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: 406
Length of database: 434
Length adjustment: 32
Effective length of query: 374
Effective length of database: 402
Effective search space:   150348
Effective search space used:   150348
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis