Alignments for a candidate for cysK in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Rhodospirillum rubrum ATCC 11170

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 WP_011389589.1 RRU_RS09535 PLP-dependent transferase

Query= SwissProt::P06106
         (444 letters)



>NCBI__GCF_000013085.1:WP_011389589.1
          Length = 430

 Score =  375 bits (962), Expect = e-108
 Identities = 195/439 (44%), Positives = 284/439 (64%), Gaps = 17/439 (3%)

Query: 3   SHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNP 62
           +H +T+ LHAG  +  D A  + AVPIY TTSY F +++  + LF L+  G +Y+R  NP
Sbjct: 6   THPETLVLHAGYRS--DEATNAVAVPIYQTTSYQFRDTEQAANLFALKELGNIYTRIMNP 63

Query: 63  TSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISF 122
           T + LE+R+AALEGG AALAVSSGQ A T A+  L   GDN V+++ LYGGT+N F  +F
Sbjct: 64  TCDALEQRVAALEGGVAALAVSSGQTASTFAVLNLCQAGDNFVTSTDLYGGTWNLFANTF 123

Query: 123 KRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVV 182
           K+ GIEARFV+  +PE F +  DE+T+  Y ET+ NPK +V    ++ AI    G+P++V
Sbjct: 124 KQMGIEARFVDPSDPEAFRRATDEKTRCYYAETLPNPKLHVFPIAEVAAIGRALGVPLIV 183

Query: 183 DNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQ 242
           DNT  A    C+P+  GA +V +SATK+IGGHGT+IGGI+VD G F W+ +  +FP  + 
Sbjct: 184 DNT--AAPVLCRPLALGAAVVVYSATKYIGGHGTSIGGIVVDGGNFDWEAHGARFPTLTN 241

Query: 243 PAEGYHGTIYNEA---YGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERH 299
           P   YHG ++ EA    G +AYI+ +R  LLRD+G  ++PF +FLL+QG+ETL LR   H
Sbjct: 242 PDPSYHGAVWTEAVKPLGPIAYILRMRVILLRDIGAALSPFNAFLLIQGLETLPLRMRAH 301

Query: 300 GENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKET 359
            ENALK+  +L+  P V+ V +P + +          L++G G ++ F +K    A    
Sbjct: 302 CENALKVVDFLKSHPQVTTVIHPSVQTGELARRRDGALAHGQGALVGFELKGGLEA---- 357

Query: 360 DPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSV 419
                 G   +D LK+  ++AN+GDA++L I P  TTH QL+ +++LA+GV++  +R+S+
Sbjct: 358 ------GRAFIDALKMLYHVANIGDARSLAIHPASTTHSQLSAEDQLATGVSQGYVRLSI 411

Query: 420 GIEFIDDIIADFQQSFETV 438
           GIE  DDII D +Q+ E++
Sbjct: 412 GIEHADDIIGDLKQALESL 430


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: 484
Number of extensions: 11
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: 430
Length adjustment: 32
Effective length of query: 412
Effective length of database: 398
Effective search space:   163976
Effective search space used:   163976
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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

GapMind for Amino acid biosynthesis