Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate Pf6N2E2_3321 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= BRENDA::Q2V0C9 (504 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3321 Length = 317 Score = 173 bits (439), Expect = 7e-48 Identities = 101/288 (35%), Positives = 161/288 (55%), Gaps = 7/288 (2%) Query: 64 IYAKCEFLNPGGSVKDRIAYRMIQDAEDKGLLKPGCTIIEPTSGNTGIGLAMAAAVRGYK 123 +Y K E LNP GS+K + A +I+++E GLL PG +IE +SGN G+ L+M A RGY Sbjct: 22 VYLKIEGLNPAGSIKLKTAISLIEESERLGLLSPGRKVIESSSGNLGVALSMICAQRGYP 81 Query: 124 CIIVMPEKMSDEKISTLYALGAKIIRTPT-EASWHSPEAHISVAQKLQKEIPNSIILDQY 182 + ++ ++ + A GA++I T + + A I++ Q++ ++ P +QY Sbjct: 82 FTCITDPNVNQVSVNLMKAYGAEVIVCDTRDRNGGFLGARITLIQEMIRQDPRYFWTNQY 141 Query: 183 TNPGNPLAHYDQTAIEIWKQCEGKIDYLVAGAGTGGTISGIGRKLKELSPNIKIIAVDPK 242 NP NPLAHY++TA EI +Q +L GAGT GT+ G R L+E +P +K+IAVD Sbjct: 142 ANPANPLAHYNRTAPEILQQ-HPNCKWLFVGAGTTGTLIGCARYLREKAPEVKLIAVDTV 200 Query: 243 GSILDPSSDSQNEVGFYEVEGIGYDFIPTVLDRNVIDKWIKTEDNESLNAARMLIRQEGL 302 GSI + Q + G+G P +L+R++++ ++ E++ R + + GL Sbjct: 201 GSI-----NFQEVPKKRLIPGLGTSRRPEILERDLVEHIEFVDEVETIRMCRSVAQDYGL 255 Query: 303 LCGGSSGAALIAALKIAKDIPEEKRMVIILPDGIRNYLTKFVSEYWME 350 L GGS+G L+A ++ K IP +V+I PD YL S+ W + Sbjct: 256 LLGGSTGTVLVAVKRLRKQIPAGDEVVVISPDMGERYLETIYSDKWCD 303 Lambda K H 0.318 0.135 0.404 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: 354 Number of extensions: 21 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: 504 Length of database: 317 Length adjustment: 31 Effective length of query: 473 Effective length of database: 286 Effective search space: 135278 Effective search space used: 135278 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 (21.7 bits) S2: 50 (23.9 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