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 7026046 Shewana3_3188 cysteine synthase B (RefSeq)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__ANA3:7026046 Length = 292 Score = 187 bits (475), Expect = 3e-52 Identities = 111/308 (36%), Positives = 171/308 (55%), Gaps = 17/308 (5%) Query: 1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIE 60 M+ + ++ +G TPLV LQRL D + KLE NP GS+KDR A+ MI Sbjct: 1 MSDFPTIEACIGQTPLVRLQRL--------DCGSSTVLLKLEGNNPAGSVKDRAALNMII 52 Query: 61 QAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQI 120 QAE + PG T++E TSGNTGI+LAMAA +KGY++I +MP N++ ER+ ++ YGA++ Sbjct: 53 QAELRQEIAPGDTLIEATSGNTGIALAMAAAIKGYKMILIMPSNSTQERKDAMQAYGAEL 112 Query: 121 IFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHF 179 + A A +L A V L Q+ N N ++H+ TGPE+ +ITHF Sbjct: 113 LL---VDNMEAARDLALDLQAQGKGKV-LDQFNNQDNANAHFQTTGPEIWQQSQGKITHF 168 Query: 180 VAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTAR 239 V+ +GTTGT+MG ++L+ ++ IV +P G + +R + ++P ++D + A Sbjct: 169 VSSMGTTGTIMGVSKYLKSRNPDITIVGLQPADGSSIPGIRRWPQEYLPGIFDAARVDAV 228 Query: 240 YSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWK 299 + DA R L EGI AG+S+G + AAL + + + +V D G + Sbjct: 229 MDIEEQDAKAMARTLAREEGICAGVSSGGAVFAALEIA----RQNPGSVVVAIVCDRGDR 284 Query: 300 YLSTGAYA 307 YLS+G ++ Sbjct: 285 YLSSGLFS 292 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: 254 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: 292 Length adjustment: 27 Effective length of query: 296 Effective length of database: 265 Effective search space: 78440 Effective search space used: 78440 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