Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Pf6N2E2_3321 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3321 Length = 317 Score = 161 bits (407), Expect = 2e-44 Identities = 97/281 (34%), Positives = 155/281 (55%), Gaps = 19/281 (6%) Query: 27 VQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGSTIIEATSGNTGIGLAMIGRVKG 86 V +Y K+EG NP GS+K + A+ +IE++E G L PG +IE++SGN G+ L+MI +G Sbjct: 20 VPVYLKIEGLNPAGSIKLKTAISLIEESERLGLLSPGRKVIESSSGNLGVALSMICAQRG 79 Query: 87 YNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDG----AIRKVAELVKENPGKYFNP 142 Y + V+ ++KA+GAE+I+ D + G I + E+++++P +YF Sbjct: 80 YPFTCITDPNVNQVSVNLMKAYGAEVIVCDTRDRNGGFLGARITLIQEMIRQDP-RYFWT 138 Query: 143 NQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLMGVGKNLREKNPEIKIIEA 202 NQ++N N +AHY TA EI Q FV A GT+GTL+G + LREK PE+K+I Sbjct: 139 NQYANPANPLAHYNRTAPEILQQHPNCKWLFVGA-GTTGTLIGCARYLREKAPEVKLIAV 197 Query: 203 ---------QPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAFAKAREIVAQEG 253 + K I GL + P I + D ++ ++ E R + G Sbjct: 198 DTVGSINFQEVPKKRLIPGLGTSRR---PEILERDLVEHIEFVDEVETIRMCRSVAQDYG 254 Query: 254 IFIGMSSGAAMLAAQKLAEKIDSG-VIVVLFADRGEKYLST 293 + +G S+G ++A ++L ++I +G +VV+ D GE+YL T Sbjct: 255 LLLGGSTGTVLVAVKRLRKQIPAGDEVVVISPDMGERYLET 295 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: 268 Number of extensions: 18 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: 299 Length of database: 317 Length adjustment: 27 Effective length of query: 272 Effective length of database: 290 Effective search space: 78880 Effective search space used: 78880 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