Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Synpcc7942_1466 Synpcc7942_1466 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__SynE:Synpcc7942_1466 Length = 334 Score = 212 bits (540), Expect = 8e-60 Identities = 122/307 (39%), Positives = 178/307 (57%), Gaps = 13/307 (4%) Query: 2 IYDNILETIGNTPLVRINHLN--PNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGK 59 I NI E IG TPLV++N + ++ KLE FNP+ SVKDRI + MI +AE +G Sbjct: 17 IAQNITELIGRTPLVQLNRIPVADGCLARIVVKLESFNPSASVKDRIGISMILEAERKGL 76 Query: 60 LHPG-STIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKK 118 + P +T++E TSGNTGI LAM +GY +I+ M + +S ERR M++A+GA + LT Sbjct: 77 IAPDRTTLVEPTSGNTGIALAMAAAARGYRLILTMPDTMSSERRAMLRAYGATLELTPGI 136 Query: 119 LGTDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVG 178 G G I++ E+V +P Y QF N N H +TTAEEIWA T GTV ++ VG Sbjct: 137 EGMAGCIQRAQEIVASHPEAYM-LQQFKNPANPKIHRETTAEEIWADTDGTVDILISGVG 195 Query: 179 TSGTLMGVGKNLREKNPEIKIIEAQPTKGHYIQG-------LKSMEEAIVPAIYQADKID 231 T GT+ GV + L+E+ P + +P + G ++ + VP + ID Sbjct: 196 TGGTITGVAEVLKERKPSFQAFAVEPANSPVLSGGRPGPHKIQGIGAGFVPEVLATQLID 255 Query: 232 EHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDS--GVIVVLFADRGEK 289 E + + +EA A R + +EG+ G+SSGAA+ AA ++A + ++ +IVV+ GE+ Sbjct: 256 EVVTVSDDEAIAYGRRLAREEGLLSGISSGAAVAAAVQVARRPENTDKLIVVILPSFGER 315 Query: 290 YLSTKLF 296 YLST LF Sbjct: 316 YLSTPLF 322 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: 279 Number of extensions: 15 Number of successful extensions: 7 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: 334 Length adjustment: 27 Effective length of query: 272 Effective length of database: 307 Effective search space: 83504 Effective search space used: 83504 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