GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Sinorhizobium meliloti 1021

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate SMc01666 SMc01666 methionine gamma-lyase

Query= SwissProt::P9WGB5
         (406 letters)



>FitnessBrowser__Smeli:SMc01666
          Length = 427

 Score =  192 bits (488), Expect = 2e-53
 Identities = 129/395 (32%), Positives = 207/395 (52%), Gaps = 37/395 (9%)

Query: 40  MYLTSGYVYGSAAVAEKSF----------AGELDHYVYSRYGNPTVSVFEERLRLIEGAP 89
           ++LTS +V+ SA      F          AG     VYSR+ +P   + E+RL + E A 
Sbjct: 40  IFLTSTFVFHSAEEGRDFFDFVSGRREPPAGVGAGLVYSRFNHPNSEIVEDRLAIFERAE 99

Query: 90  AAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTV-FVDGDDL 148
           A    +SGM+A+ T+L A +  GD ++ ++ L+G    + ++     GV  V F DG D 
Sbjct: 100 AGALFSSGMSAIATTLLAFVRPGDSILHSQPLYGGTETLLAKTFLNLGVSAVGFADGTDE 159

Query: 149 SQW----ERALSVP-TQAVFFETPSNPMQSLVDIAAVTELAHAAGAK------VVLDNVF 197
           +      E A+S      +  ETP+NP  SLVD+A V  +A   G +      V  DN  
Sbjct: 160 AAVNAAAEEAMSKGRVSVILIETPANPTNSLVDVALVRRIAERIGERQAHRPIVACDNTL 219

Query: 198 ATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAF 257
             P+ Q     G D+ +YS TK++ G   ++ GA+LG +  I   V+ L    G  +   
Sbjct: 220 LGPVFQHPIEHGADLSLYSLTKYVGGHSDLIAGAVLGSKALIR-QVKALRGSIGTQLDPH 278

Query: 258 NAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSH----PQYDLAKRQ 313
           + W++ + LETL++R++ +N +A+ +AEFL  HP V   R  YLP H    P   +   Q
Sbjct: 279 SCWMIGRSLETLSVRMEKANDNARIVAEFLRDHPKVE--RIHYLPFHDADTPVGRVFATQ 336

Query: 314 MSGGGTVVTFALDCPEDVA--KQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMG 371
            +G G+  +F      D+A  ++ AF  L+ +++  ++ +LG  +SL +HPA  TH  + 
Sbjct: 337 CTGAGSTFSF------DIAGGQEAAFRFLNALQIFKLAVSLGGTESLASHPAAMTHSGVP 390

Query: 372 PEGRAAIGLGDGVVRISVGLEDTDDLIADIDRALS 406
            E RA IG+ +  +R+S+G+E  DDL+AD+  AL+
Sbjct: 391 IEVRARIGVLESTIRLSIGIEHPDDLVADVANALT 425


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: 457
Number of extensions: 35
Number of successful extensions: 5
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: 427
Length adjustment: 31
Effective length of query: 375
Effective length of database: 396
Effective search space:   148500
Effective search space used:   148500
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