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 3608924 Dshi_2314 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Dino:3608924 Length = 345 Score = 112 bits (279), Expect = 2e-29 Identities = 98/324 (30%), Positives = 148/324 (45%), Gaps = 35/324 (10%) Query: 1 MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIE 60 M Y L +A+G+TPL+ L S + + K E NP S+KDR A+ +I Sbjct: 1 MHSYRDLAEAIGHTPLIRLNAAS-------EATGCEILGKAEFLNPGQSVKDRAALYIIR 53 Query: 61 QAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQI 120 A A G L+PG TI+E T+GNTGI LA+ G++ + V+PE S E++ +L L GA + Sbjct: 54 DAVARGTLKPGGTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGADL 113 Query: 121 IFSAAEGGSNT------AVATAKELAATNP-SWVMLYQYGNPANTDSHYCGTGPELLADL 173 + A N + AK LA T P + Q+ N AN +H TGPE+ Sbjct: 114 VQVPAAPYRNPNNYVRYSERLAKRLAETEPHGAIWANQFDNVANRQAHVETTGPEIWDQT 173 Query: 174 -PEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDE-----GFV 227 ++ F+ G+ GT+ G G L+ VK+ A+P G +Y E + Sbjct: 174 GGKVDGFICAAGSGGTVAGVGLALQP--KGVKVGLADPD-GAALYNFYTQGELKSEGSSI 230 Query: 228 PELYDPEILTARY---------SVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGA 278 E +TA +V +A+ +L+ EGI G S+G + A+ + Sbjct: 231 SEGIGQGRITANLEGFTPDFACNVPDSEALPIVFDLLRHEGICLGGSSGINIAGAIRM-- 288 Query: 279 GALAAGERADIALVVADAGWKYLS 302 A G I ++ D G +Y S Sbjct: 289 -ARHMGPGHTIVTILCDYGTRYQS 311 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: 308 Number of extensions: 14 Number of successful extensions: 2 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 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