Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate CA265_RS13740 CA265_RS13740 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Pedo557:CA265_RS13740 Length = 348 Score = 199 bits (506), Expect = 8e-56 Identities = 117/312 (37%), Positives = 181/312 (58%), Gaps = 18/312 (5%) Query: 3 YDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHP 62 ++++ +GNTP++ + + ++Y K E +N TGS+KDR+AL +++A AEGK+ Sbjct: 17 FEHLSLLVGNTPMLELTYTYQGSLGKIYVKCEHYNLTGSIKDRMALYTLKKAYAEGKIKA 76 Query: 63 GSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTD 122 G I+EATSGNTGI A IG+ G+ V I+M +S ER +IK+ GAEIIL K+ G Sbjct: 77 GDRIVEATSGNTGIAFAAIGKALGHPVTIIMPNWLSKERMDIIKSLGAEIILVSKEEGGF 136 Query: 123 GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTK---GTVTHFVAAVGT 179 K+AE + + F P QF N N AH TT +EIW Q + + FVA VGT Sbjct: 137 IGSIKLAEKMAASDPNIFLPKQFENIANPEAHEHTTGKEIWEQLRLKNLSPDAFVAGVGT 196 Query: 180 SGTLMGVGKNLREKNPEIKIIEAQPTK-----------GHYIQGLKSMEEAIVPAIYQAD 228 GT+MGVG LR++N +IKI +P + H IQG+ + +P I + + Sbjct: 197 GGTIMGVGNFLRKQNADIKIHPLEPAESPTLTTGYKVGSHRIQGI---SDEFIPEIVKLN 253 Query: 229 KIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDS-GVIVVLFADRG 287 ++DE + + +A A+++ + G+ +G+SSGA ++ A K +K+ + +V +F+D Sbjct: 254 ELDEVLQVNDGDAILMAQKLAEKLGLAVGISSGANVIGAIKQQQKMGADSCVVTIFSDSN 313 Query: 288 EKYLSTKLFDTE 299 +KYLST L E Sbjct: 314 KKYLSTDLMKVE 325 Lambda K H 0.315 0.133 0.367 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: 288 Number of extensions: 19 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: 299 Length of database: 348 Length adjustment: 28 Effective length of query: 271 Effective length of database: 320 Effective search space: 86720 Effective search space used: 86720 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: 42 (22.0 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