GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metC in Dyella japonica UNC79MFTsu3.2

Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate N515DRAFT_4305 N515DRAFT_4305 cystathionine gamma-lyase

Query= SwissProt::Q83A83
         (387 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4305 N515DRAFT_4305
           cystathionine gamma-lyase
          Length = 392

 Score =  513 bits (1320), Expect = e-150
 Identities = 242/377 (64%), Positives = 303/377 (80%), Gaps = 1/377 (0%)

Query: 11  IDTRVIHAGQKPDPLTGAVMTPIYTASTYAQKSPGVHQGYEYSRSQNPTRFAYERCVADL 70
           + T  IHAGQ PDP TGA+MTPIY  STY Q+SPG H+GYEYSR+QNPTR AYE CVA L
Sbjct: 16  LGTLAIHAGQSPDPTTGAIMTPIYATSTYVQESPGKHKGYEYSRTQNPTRMAYEACVAAL 75

Query: 71  ESGQHGFAFASGMAATATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAGLSFSFVDF 130
           E G  GFAF SG+AA AT+L+LL  G HV+ MDD+YGGSYRLFE VR+RSAGL F+FVD 
Sbjct: 76  EGGVAGFAFGSGLAAAATVLDLLDSGSHVIAMDDLYGGSYRLFERVRRRSAGLDFTFVDL 135

Query: 131 TDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTFATPIIQRP 190
            D   ++ A+   TKM+W E+P+NP LK+VDLAK+A  AK+  +I V DNTF +P+IQRP
Sbjct: 136 NDAQALKAALKPNTKMIWAETPTNPMLKLVDLAKVAAFAKKHGLILVVDNTFCSPMIQRP 195

Query: 191 LELGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKYLQNAIGAIAAPFDSFMVLR 250
            E G D+V HSATKYLNGHSD++GG+ VV   + LAE++ +LQN++GA+A PFDSF+ +R
Sbjct: 196 FESGADLVLHSATKYLNGHSDMVGGI-VVAREQELAERMGFLQNSVGAVAGPFDSFLAMR 254

Query: 251 GLKTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMISVE 310
           GLKTL +RM+ HCE+A++LAQWLEKHP+V+RV YPGL SHPQH++A++QM  FGG+IS+E
Sbjct: 255 GLKTLHLRMKAHCESALELAQWLEKHPEVERVIYPGLKSHPQHALARRQMHGFGGIISIE 314

Query: 311 LKCDLNETKKVLERCQLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLS 370
           +K  L + +++LERC LF LAESLGGVESLIEHPAIMTHAS+P A R++LGI+D  IRLS
Sbjct: 315 VKGGLRKARRMLERCHLFALAESLGGVESLIEHPAIMTHASVPPANRKRLGISDSLIRLS 374

Query: 371 VGIEAITDLRHDLEAAL 387
           VG+E I DLR +L  AL
Sbjct: 375 VGVEDIADLRSELAEAL 391


Lambda     K      H
   0.319    0.134    0.385 

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: 461
Number of extensions: 10
Number of successful extensions: 2
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: 387
Length of database: 392
Length adjustment: 30
Effective length of query: 357
Effective length of database: 362
Effective search space:   129234
Effective search space used:   129234
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see 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