GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Marinobacter adhaerens HP15

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 GFF1863 HP15_1820 methionine gamma-lyase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__Marino:GFF1863
          Length = 413

 Score =  260 bits (664), Expect = 7e-74
 Identities = 159/433 (36%), Positives = 233/433 (53%), Gaps = 49/433 (11%)

Query: 6   DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65
           DT+ + AGQ   G   H      I+ T+S+V+ ++   +  FG E PG +YSRF NPT  
Sbjct: 22  DTLAVRAGQIRTGQLEHSDA---IFPTSSFVYGSAAQAAARFGGEEPGNIYSRFTNPTVQ 78

Query: 66  VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125
             E RIAA+EGG  A+A +SG +A       L  +GD+++ +  ++G T   F+    RF
Sbjct: 79  AFEGRIAAMEGGERAVATASGMSAILSTCMALLKSGDHVICSRGVFGTTNVLFQKYMARF 138

Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185
           G+E  FV   + EE++      T+ +++ET  NP   V D E +  +A  +    VVDN 
Sbjct: 139 GVETTFVSLTDMEEWQASIRSETRMLFIETPSNPLCEVADMEILGQLARDNDALFVVDNC 198

Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245
           F       +P++ GADIV HSATK++ G G  +GG++V S K                  
Sbjct: 199 F-CTPVLQRPLEQGADIVIHSATKYLDGQGRCVGGVVVGSEK------------------ 239

Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305
                +  E YG            LR  GP M+PF +++  +G+ETL +R   H +NAL+
Sbjct: 240 -----MMEEVYG-----------FLRSAGPTMSPFNAWVFQKGLETLPIRMRAHCDNALE 283

Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365
           LA WLEQ P V  V Y GL SH  HE AKK    GFGGVLSF +K    A +E   F   
Sbjct: 284 LALWLEQQPAVERVFYAGLQSHPQHELAKKQ-QTGFGGVLSFQLK---GAREEAWRF--- 336

Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425
               +D  ++ S  AN+GD KT +  P  TTH +L+ ++K  +G+T++LIR+SVGIE ++
Sbjct: 337 ----IDGTRMISITANLGDVKTTITHPATTTHGRLSPEDKARAGITENLIRISVGIEAVE 392

Query: 426 DIIADFQQSFETV 438
           D+  D ++ F+ +
Sbjct: 393 DLKTDLERGFQAL 405


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: 451
Number of extensions: 18
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: 444
Length of database: 413
Length adjustment: 32
Effective length of query: 412
Effective length of database: 381
Effective search space:   156972
Effective search space used:   156972
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