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 SMc01809 SMc01809 O-acetylhomoserine aminocarboxypropyltransferase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__Smeli:SMc01809
          Length = 426

 Score =  382 bits (981), Expect = e-110
 Identities = 200/430 (46%), Positives = 275/430 (63%), Gaps = 14/430 (3%)

Query: 5   FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64
           F T+ +HAG +   D    +RA PIY TTS+VF ++ H + LFGL+  G +Y+R  NPT 
Sbjct: 7   FSTLAIHAGAQP--DPTTGARATPIYQTTSFVFNDTDHAAALFGLQQFGNIYTRIMNPTQ 64

Query: 65  NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124
            VLEERIAALEGG A LAVSSG AAQ L    +   GDN VS   LYGG+ NQF  +FK 
Sbjct: 65  AVLEERIAALEGGTAGLAVSSGHAAQLLVFHTIMRPGDNFVSARQLYGGSANQFGHAFKA 124

Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184
           F  + R+ +   PE F+   DERTKA+++E++ NP     D   I  +A +HG+P++VDN
Sbjct: 125 FDWQVRWADSAEPESFDAQIDERTKAIFIESLANPGGTFVDIAAIADVARRHGLPLIVDN 184

Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244
           T  A  Y  +P+++GADIV HS TK+IGGHG ++GGIIVD G F W     K+P  S+P 
Sbjct: 185 TM-ATPYLMRPLEHGADIVVHSLTKFIGGHGNSMGGIIVDGGTFDWSK-SGKYPLLSEPR 242

Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304
             Y G + ++A+GN A+ +  R   LRD GP ++PF +FL+  GVETL LR +RH +NAL
Sbjct: 243 PEYGGVVLHQAFGNFAFAIAARVLGLRDFGPAISPFNAFLIQTGVETLPLRMQRHCDNAL 302

Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364
           ++AKWL+    VSWV Y GL    +H   K+Y   G G V +FG+     A         
Sbjct: 303 EVAKWLKGHEKVSWVRYSGLEDDPNHALQKRYSPKGAGAVFTFGLAGGYEA--------- 353

Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424
            G + V+ L++ S+LAN+GD ++LVI P  TTH+QL  ++++A+G   D+IR+SVGIE +
Sbjct: 354 -GKRFVEALEMFSHLANIGDTRSLVIHPASTTHRQLTPEQQVAAGAGPDVIRLSVGIEDV 412

Query: 425 DDIIADFQQS 434
            DIIAD +Q+
Sbjct: 413 ADIIADLEQA 422


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: 535
Number of extensions: 21
Number of successful extensions: 4
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: 426
Length adjustment: 32
Effective length of query: 412
Effective length of database: 394
Effective search space:   162328
Effective search space used:   162328
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