GapMind for Amino acid biosynthesis

 

Alignments for a candidate for Mt_cysM in Streptacidiphilus oryzae TH49

Align [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized)
to candidate WP_037575993.1 BS73_RS24550 cysteine synthase

Query= BRENDA::P9WP53
         (323 letters)



>NCBI__GCF_000744815.1:WP_037575993.1
          Length = 322

 Score =  457 bits (1177), Expect = e-133
 Identities = 230/322 (71%), Positives = 262/322 (81%), Gaps = 2/322 (0%)

Query: 3   RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQA 62
           RY+S LQA+GNTPLVGL R+S   D G +   VR+WAKLEDRNPTGS+KDRPA+ MIE+A
Sbjct: 2   RYESPLQAVGNTPLVGLPRISAEID-GNESGDVRIWAKLEDRNPTGSVKDRPALNMIERA 60

Query: 63  EADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF 122
           EA+G + PG TILEPTSGNTGISLAMAA+LKGYR++CVMPENTS ERR+LL ++GA++I 
Sbjct: 61  EAEGRISPGDTILEPTSGNTGISLAMAAKLKGYRMVCVMPENTSEERRELLRMWGAEVIP 120

Query: 123 SAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAG 182
           S A GGSNTAV  AKELA  +P WVMLYQYGN  N  +HY GTGPE+LADLP +THFVAG
Sbjct: 121 SPAAGGSNTAVRVAKELAEEHPDWVMLYQYGNADNAGAHYSGTGPEILADLPTVTHFVAG 180

Query: 183 LGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSV 242
           LGTTGTLMG GR+LRE V  VKIVAAEPRY + VY LRN+DEGFVPELYD E+LT RYSV
Sbjct: 181 LGTTGTLMGVGRYLREKVPGVKIVAAEPRYDDLVYGLRNLDEGFVPELYDAEVLTTRYSV 240

Query: 243 GAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLS 302
           G+ DAVRRTREL+  EGIFAGISTGA LHAA GV   A  AGERAD+  VVAD GWKYLS
Sbjct: 241 GSADAVRRTRELLQLEGIFAGISTGAALHAACGVARKAATAGERADVVFVVADGGWKYLS 300

Query: 303 TGAY-AGSLDDAETALEGQLWA 323
           TG Y A + + A   L+GQLWA
Sbjct: 301 TGVYTAETTEAAIETLQGQLWA 322


Lambda     K      H
   0.317    0.134    0.398 

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: 426
Number of extensions: 13
Number of successful extensions: 3
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: 323
Length of database: 322
Length adjustment: 28
Effective length of query: 295
Effective length of database: 294
Effective search space:    86730
Effective search space used:    86730
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: 48 (23.1 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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