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_011384252.1 AMB_RS09340 CBS domain-containing protein
Query= BRENDA::P9WP53 (323 letters) >NCBI__GCF_000009985.1:WP_011384252.1 Length = 455 Score = 159 bits (402), Expect = 1e-43 Identities = 114/321 (35%), Positives = 164/321 (51%), Gaps = 38/321 (11%) Query: 4 YDS-LLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQA 62 YD+ LL +GNTPL+ L L D RL+ KLE RNP+GSIKDR A+ M+ A Sbjct: 3 YDADLLCQIGNTPLIELTNL--------DTAPCRLFVKLESRNPSGSIKDRAALSMVRAA 54 Query: 63 EADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF 122 E DGLLRPG ++E T+GNTG++LA+ A +GYRL V+P+ +++ L GA+++ Sbjct: 55 ERDGLLRPGGHLVEATAGNTGLALALLAAHRGYRLTLVIPDKAGLDKVSHLRAMGAEVVL 114 Query: 123 SAA-------EGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADL-P 174 + + E N A A E A + Q+ NPAN +H GTGPEL + Sbjct: 115 ARSDVPRRHPEHYQNVASRLAGETGAH-----FIDQFNNPANPAAHEDGTGPELWEQMGG 169 Query: 175 EITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEP------------RYGE-GVYALRN 221 + VAG G+ GTL G RF ++V A+P R GE G + + Sbjct: 170 RVDAVVAGAGSGGTLTGLSRFFARRSPATEMVLADPRGSVLADYVRTGRVGEAGSWLVEG 229 Query: 222 MDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGAL 281 + +P + D +T YSV ++ R ++ EG+ G S+G +L AAL Sbjct: 230 IGGDSIPMVSDFSRVTRAYSVSDRESFATARLVLRIEGLLVGSSSGTLLAAALRYCREQT 289 Query: 282 AAGERADIALVVADAGWKYLS 302 A +A +V DAG ++LS Sbjct: 290 APKR---VATLVCDAGNRHLS 307 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: 366 Number of extensions: 15 Number of successful extensions: 5 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: 455 Length adjustment: 30 Effective length of query: 293 Effective length of database: 425 Effective search space: 124525 Effective search space used: 124525 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 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