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 Pf6N2E2_3321 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3321 Length = 317 Score = 139 bits (350), Expect = 9e-38 Identities = 89/285 (31%), Positives = 140/285 (49%), Gaps = 25/285 (8%) Query: 35 VRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKG 94 V ++ K+E NP GSIK + A+ +IE++E GLL PG ++E +SGN G++L+M +G Sbjct: 20 VPVYLKIEGLNPAGSIKLKTAISLIEESERLGLLSPGRKVIESSSGNLGVALSMICAQRG 79 Query: 95 YRLICVMPENTSVERRQLLELYGAQIIFSAAE----GGSNTAVATAKELAATNPSWVMLY 150 Y C+ N + L++ YGA++I G + +E+ +P + Sbjct: 80 YPFTCITDPNVNQVSVNLMKAYGAEVIVCDTRDRNGGFLGARITLIQEMIRQDPRYFWTN 139 Query: 151 QYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAE- 209 QY NPAN +HY T PE+L P G GTTGTL+G R+LRE VK++A + Sbjct: 140 QYANPANPLAHYNRTAPEILQQHPNCKWLFVGAGTTGTLIGCARYLREKAPEVKLIAVDT 199 Query: 210 -----------PRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTE 258 R G+ R PE+ + +++ V V+ +R R + Sbjct: 200 VGSINFQEVPKKRLIPGLGTSRR------PEILERDLVEHIEFVDEVETIRMCRSVAQDY 253 Query: 259 GIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLST 303 G+ G STG VL A + + AG+ ++ ++ D G +YL T Sbjct: 254 GLLLGGSTGTVLVAVKRL-RKQIPAGD--EVVVISPDMGERYLET 295 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: 254 Number of extensions: 11 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: 317 Length adjustment: 28 Effective length of query: 295 Effective length of database: 289 Effective search space: 85255 Effective search space used: 85255 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: 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