GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Sinorhizobium meliloti 1021

Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate SMc01666 SMc01666 methionine gamma-lyase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__Smeli:SMc01666
          Length = 427

 Score =  138 bits (347), Expect = 4e-37
 Identities = 118/428 (27%), Positives = 189/428 (44%), Gaps = 72/428 (16%)

Query: 28  PIYATTSYVFENSKHGSQLFGL-----EVP-----GYVYSRFQNPTSNVLEERIAALEGG 77
           PI+ T+++VF +++ G   F       E P     G VYSRF +P S ++E+R+A  E  
Sbjct: 39  PIFLTSTFVFHSAEEGRDFFDFVSGRREPPAGVGAGLVYSRFNHPNSEIVEDRLAIFERA 98

Query: 78  AAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEA-RFVEGDN 136
            A    SSG +A    +      GD+I+ +  LYGGT      +F   G+ A  F +G +
Sbjct: 99  EAGALFSSGMSAIATTLLAFVRPGDSILHSQPLYGGTETLLAKTFLNLGVSAVGFADGTD 158

Query: 137 PEEFEKVFDE-----RTKAVYLETIGNPKYNVPDFEKIVAIAHK------HGIPVVVDNT 185
                   +E     R   + +ET  NP  ++ D   +  IA +      H   V  DNT
Sbjct: 159 EAAVNAAAEEAMSKGRVSVILIETPANPTNSLVDVALVRRIAERIGERQAHRPIVACDNT 218

Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245
              G  F  PI++GAD+  +S TK++GGH   I G ++                      
Sbjct: 219 L-LGPVFQHPIEHGADLSLYSLTKYVGGHSDLIAGAVL---------------------- 255

Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305
                      G+ A I  V+  L   +G  ++P + +++ + +ETLS+R E+  +NA  
Sbjct: 256 -----------GSKALIRQVKA-LRGSIGTQLDPHSCWMIGRSLETLSVRMEKANDNARI 303

Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLS---NGFGGVLSFGVKDLPNADKETDPF 362
           +A++L   P V  + Y  L  H       +  +    G G   SF +     A  +   F
Sbjct: 304 VAEFLRDHPKVERIHY--LPFHDADTPVGRVFATQCTGAGSTFSFDI-----AGGQEAAF 356

Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422
           +   A  +   KLA +L   G  ++L   P   TH  +  + +   GV +  IR+S+GIE
Sbjct: 357 RFLNALQI--FKLAVSL---GGTESLASHPAAMTHSGVPIEVRARIGVLESTIRLSIGIE 411

Query: 423 FIDDIIAD 430
             DD++AD
Sbjct: 412 HPDDLVAD 419


Lambda     K      H
   0.317    0.136    0.402 

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: 396
Number of extensions: 23
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 444
Length of database: 427
Length adjustment: 32
Effective length of query: 412
Effective length of database: 395
Effective search space:   162740
Effective search space used:   162740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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