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 Pf1N1B4_4889 Cystathionine beta-synthase (EC 4.2.1.22)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4889 Length = 458 Score = 173 bits (438), Expect = 8e-48 Identities = 113/314 (35%), Positives = 164/314 (52%), Gaps = 28/314 (8%) Query: 6 SLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEAD 65 ++L+ +GNTPLV + R GP L+ KLE +NP GSIKDR + MI+ AE D Sbjct: 8 AVLELIGNTPLVRISRFDT-------GP-CTLFLKLESQNPGGSIKDRIGLAMIDTAERD 59 Query: 66 GLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAA 125 G LRPG TI+E T+GNTG+ LA+ R KGYR++ V+P+ S E+ L+ GA++ + + Sbjct: 60 GRLRPGGTIVEATAGNTGLGLALVGRAKGYRVVLVVPDKMSTEKVLHLKAMGAEVHITRS 119 Query: 126 E---GGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVA 181 + G + A LA P Q+ NPAN +H C T PE+ A ++ V Sbjct: 120 DVGKGHPDYYQDVAARLARDIPDAFFADQFNNPANPLAHECSTAPEIWAQTQHDVDAIVV 179 Query: 182 GLGTTGTLMGTGRFLREHVANVKIVAAEP---------RYG----EGVYALRNMDEGFVP 228 G+G+ GTL G RF + N+++V A+P R G G +A+ + E F+P Sbjct: 180 GVGSAGTLTGLTRFFQRVQPNLEMVLADPVGSVMAEYSRSGTLGTPGSWAVEGIGEDFIP 239 Query: 229 ELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERAD 288 + D + YS+ ++ R+L+ EGI G STG +L AAL E Sbjct: 240 SIADLSSVRKAYSISDEESFDHARQLLRAEGILGGSSTGTLLAAALRY---CREQTEPKR 296 Query: 289 IALVVADAGWKYLS 302 + V D G +YLS Sbjct: 297 VVSFVCDTGTRYLS 310 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: 370 Number of extensions: 17 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: 458 Length adjustment: 30 Effective length of query: 293 Effective length of database: 428 Effective search space: 125404 Effective search space used: 125404 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 Jul 25 2024. The underlying query database was built on Jul 25 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