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_011382646.1 AMB_RS01005 cysteine synthase A
Query= BRENDA::P9WP53 (323 letters) >NCBI__GCF_000009985.1:WP_011382646.1 Length = 319 Score = 196 bits (499), Expect = 5e-55 Identities = 118/311 (37%), Positives = 172/311 (55%), Gaps = 15/311 (4%) Query: 4 YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63 YDS++ +G TPLV +R++ G + KLE NP S+KDR MIE AE Sbjct: 13 YDSIIDTIGATPLVRFKRMA-----AEAGSKADIVGKLEFFNPLASVKDRIGFAMIEAAE 67 Query: 64 ADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFS 123 G L+PG TI+EPTSGNTGI+LA A KGY+LI MPE+ S+ERR++L+L GA+I+ + Sbjct: 68 VSGQLKPGGTIIEPTSGNTGIALAFVAAAKGYKLILCMPESMSLERRKMLQLLGAEIVLT 127 Query: 124 AAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADL-PEITHFVAG 182 A G AV A+EL A+ P +M Q+ N AN H T E+ D ++ V+G Sbjct: 128 PASKGMTGAVRQAEELLASTPGAIMPQQFKNEANPAIHERTTAEEIWNDTNGKVDIIVSG 187 Query: 183 LGTTGTLMGTGRFLREHVANVKIVAAEPR-------YGEGVYALRNMDEGFVPELYDPEI 235 +GT GT+ G G L+ +K+VA EP G + ++ + GFVP++ D + Sbjct: 188 VGTGGTISGIGHVLKARKPGLKMVAVEPEDSPVLSGGAPGPHKIQGIGAGFVPDILDKGV 247 Query: 236 LTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVAD 295 + +G A+ R+ EG+ GIS+GA + AAL +G+ AG+ I ++ Sbjct: 248 IDEILQIGNETALATARKAAKLEGVPVGISSGAAIAAALELGSRPENAGKL--IVAIIPS 305 Query: 296 AGWKYLSTGAY 306 +YLST + Sbjct: 306 FAERYLSTALF 316 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: 259 Number of extensions: 12 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: 323 Length of database: 319 Length adjustment: 28 Effective length of query: 295 Effective length of database: 291 Effective search space: 85845 Effective search space used: 85845 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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