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_011651596.1 RL_RS10270 cysteine synthase A
Query= BRENDA::P9WP53 (323 letters) >NCBI__GCF_000009265.1:WP_011651596.1 Length = 345 Score = 129 bits (325), Expect = 8e-35 Identities = 99/323 (30%), Positives = 154/323 (47%), Gaps = 31/323 (9%) Query: 1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIE 60 MT + S+L+A+GNTPL+ L+ S + + K E NP S+KDR A+ +I Sbjct: 1 MTFHPSVLEAIGNTPLIKLKGAS-------EATGCTILGKAEFLNPGQSVKDRAALYIIR 53 Query: 61 QAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQI 120 AE GLLRPG I+E T+GNTGI L + A+ GYR + V+PE S E++ L+L GA++ Sbjct: 54 DAERKGLLRPGGVIVEGTAGNTGIGLTLVAKALGYRTVIVIPETQSQEKKDALKLLGAEL 113 Query: 121 IFSAAEGGSN------TAVATAKELAATNPSW-VMLYQYGNPANTDSHYCGTGPELLADL 173 + A N + A++LA T P+ + Q+ N AN +H T E+ D Sbjct: 114 VEVPAVPYKNPNNYVKVSGRLAEQLAKTEPNGAIWANQFDNVANRQAHVETTAKEIWQDT 173 Query: 174 P-EITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEP-------------RYGEGVYAL 219 ++ F+ +G+ GTL G L+ A+VKI A+P EG Sbjct: 174 DGKVDGFICSVGSGGTLAGVAAGLKAFKADVKIGIADPDGAALYEFYQNGALKSEGSSIT 233 Query: 220 RNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAG 279 + +G + + Y + +A+ +LV EG+ G ST + A+ + Sbjct: 234 EGIGQGRITANLEGFTPDYAYRIPDAEALPYLFDLVENEGLCLGGSTAINIAGAVNL--- 290 Query: 280 ALAAGERADIALVVADAGWKYLS 302 A G + ++ D G +Y S Sbjct: 291 ARDLGPGHTVVTILCDYGNRYQS 313 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: 291 Number of extensions: 11 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: 345 Length adjustment: 28 Effective length of query: 295 Effective length of database: 317 Effective search space: 93515 Effective search space used: 93515 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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