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 206086 DVU0663 cysteine synthase A
Query= BRENDA::P9WP53 (323 letters) >MicrobesOnline__882:206086 Length = 308 Score = 208 bits (529), Expect = 2e-58 Identities = 119/310 (38%), Positives = 175/310 (56%), Gaps = 17/310 (5%) Query: 6 SLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEAD 65 S+ +G TP+V L +++ G + AKLE+ NP S+KDR A+ M+E A A Sbjct: 6 SMTDLVGKTPMVRLNKVTL-------GCVAEVVAKLENFNPCSSVKDRIALNMVEAAIAR 58 Query: 66 GLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAA 125 G + PGA ++EPTSGNTG+ LA ++G +L+ MPE+ S ERR LL+ +G ++ + A Sbjct: 59 GEIAPGAVLVEPTSGNTGVGLAFVCAVRGLKLVLTMPESMSAERRALLKAFGTTLVLTPA 118 Query: 126 EGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLG 184 G AV A+ + A P VML Q+ NP N +H TGPE+ AD I FVAG+G Sbjct: 119 AKGMRGAVEEAERIVADTPGAVMLQQFANPDNPAAHEATTGPEIWADTDGMIDCFVAGVG 178 Query: 185 TTGTLMGTGRFLREHVANVKIVAAEPRY-------GEGVYALRNMDEGFVPELYDPEILT 237 T GT+ GTGR+L+ +++++A EP G +A++ + GFVP + D + Sbjct: 179 TGGTITGTGRYLKGRNPDIRVIAVEPAESAVLSGGAPGPHAIQGIGAGFVPPVLDTSVYD 238 Query: 238 ARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAG 297 V DA+ R L+ EGI GIS+GA +HAA+ AG+R + ++ D G Sbjct: 239 EVMPVPGADALTMARRLLQEEGILCGISSGANVHAAIAYARRPENAGKR--VVCIICDTG 296 Query: 298 WKYLSTGAYA 307 +YLST +A Sbjct: 297 ERYLSTPLFA 306 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: 287 Number of extensions: 16 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: 308 Length adjustment: 27 Effective length of query: 296 Effective length of database: 281 Effective search space: 83176 Effective search space used: 83176 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