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 GFF810 HP15_789 cysteine synthase B
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Marino:GFF810 Length = 297 Score = 220 bits (561), Expect = 3e-62 Identities = 123/300 (41%), Positives = 177/300 (59%), Gaps = 13/300 (4%) Query: 11 LGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRP 70 +G+TPLV LQRL + + AKLE NP GS+KDRPA+ MI++AE G ++P Sbjct: 10 VGHTPLVRLQRLPGETSNV-------ILAKLEGNNPAGSVKDRPAISMIQEAERRGDIKP 62 Query: 71 GATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSN 130 G T++E TSGNTGI+LAMAA +KGYR++ +MP N S ERR + YGA+I+ E G Sbjct: 63 GDTLIEATSGNTGIALAMAAAIKGYRMVLIMPANMSEERRASMRAYGAEIVTVTREEGME 122 Query: 131 TAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADL-PEITHFVAGLGTTGTL 189 TA A ++ A V L Q+ N N +HY TGPE+ +THFV+ +GTTGT+ Sbjct: 123 TARDLALKMQAEGKGTV-LDQFSNQDNPLAHYRTTGPEIWEQTGGRVTHFVSSMGTTGTI 181 Query: 190 MGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVR 249 MG R+L+E +++I+ +P+ G + +R E ++P++YD + VG +A Sbjct: 182 MGVSRYLKERNPDIRIIGLQPKEGASIPGIRRWPEAYLPKIYDAARVDQVLDVGQEEAET 241 Query: 250 RTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGS 309 R L EGIF G+S+G + AAL + E A I ++ D G +YLSTG + G+ Sbjct: 242 TMRALASEEGIFCGVSSGGSIAAALKLSQQV----ENAIIVAIICDRGDRYLSTGVFPGA 297 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: 305 Number of extensions: 12 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: 297 Length adjustment: 27 Effective length of query: 296 Effective length of database: 270 Effective search space: 79920 Effective search space used: 79920 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