GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Burkholderia phytofirmans PsJN

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 BPHYT_RS33835 BPHYT_RS33835 O-succinylhomoserine sulfhydrylase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__BFirm:BPHYT_RS33835
          Length = 396

 Score =  249 bits (635), Expect = 1e-70
 Identities = 151/431 (35%), Positives = 229/431 (53%), Gaps = 45/431 (10%)

Query: 4   HFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPT 63
           +FDT+ + +G      N H      I+ T+S+VFE++   ++ F      Y YSRF NPT
Sbjct: 6   NFDTLAVRSGTVRSDFNEHSEA---IFLTSSFVFESAADAAEKFKNSEDNYTYSRFTNPT 62

Query: 64  SNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFK 123
            ++ ++R+AALEGG A +A +SG AA    +      GD++VS+  L+G T   F   F 
Sbjct: 63  VSMFQDRLAALEGGEACMATASGMAAIMSVVMSTLQAGDHLVSSQALFGSTLGMFSQIFS 122

Query: 124 RFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVD 183
           +FGI   FV+  + + ++      TK  +LET  NP   V D E I  IA+      VVD
Sbjct: 123 KFGITTTFVDPTDLDAWKNAVRPETKMFFLETPSNPLTEVADIEAISKIANASNALFVVD 182

Query: 184 NTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQP 243
           N F       QP+K GAD+V HSATK++ G G  +GG +V S +F  +   + FP     
Sbjct: 183 NCF-CSPALQQPLKLGADVVMHSATKFLDGQGRVLGGALVGSKQFIME---KVFP----- 233

Query: 244 AEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENA 303
                                     +R  GP ++ F +++LL+G+ETLSLR E+   NA
Sbjct: 234 -------------------------FVRSAGPTLSAFNAWVLLKGMETLSLRVEKQSANA 268

Query: 304 LKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVK-DLPNADKETDPF 362
           L++A+WLE  P V+ V YPGL SH  H  A +    G G +LSF +K D P      +  
Sbjct: 269 LEIARWLEAHPAVNRVFYPGLESHPQHALAMRQQKAG-GAILSFELKGDTP------EQM 321

Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422
           + +  +V+DN K+ S   N+GD +T +  P  TTH ++  + + A+G+++ LIR++VG+E
Sbjct: 322 RANAWRVIDNTKICSITGNLGDTRTTITHPATTTHGRVTPEARAAAGISEGLIRLAVGLE 381

Query: 423 FIDDIIADFQQ 433
              DI  D ++
Sbjct: 382 NAGDIRGDLER 392


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: 418
Number of extensions: 18
Number of successful extensions: 4
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: 396
Length adjustment: 32
Effective length of query: 412
Effective length of database: 364
Effective search space:   149968
Effective search space used:   149968
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: 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