Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Pf6N2E2_3321 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= BRENDA::P9WP55 (310 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3321 Length = 317 Score = 163 bits (413), Expect = 4e-45 Identities = 98/277 (35%), Positives = 155/277 (55%), Gaps = 7/277 (2%) Query: 30 IVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYR 89 + K+E NPA S+K + +++++ +E+ GL+ P ++E +SGN G+AL+M+CA RGY Sbjct: 22 VYLKIEGLNPAGSIKLKTAISLIEESERLGLLSPGRKVIESSSGNLGVALSMICAQRGYP 81 Query: 90 CVLTMPETMSLERRMLLRAYGAELILTPGAD---GMSGA-IAKAEELAKTDQRYFVPQQF 145 ++ L++AYGAE+I+ D G GA I +E+ + D RYF Q+ Sbjct: 82 FTCITDPNVNQVSVNLMKAYGAEVIVCDTRDRNGGFLGARITLIQEMIRQDPRYFWTNQY 141 Query: 146 ENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGTITGVAQVIKERKPSARFVAVEPA 205 NPANP H TA E+ + + V G GT GT+ G A+ ++E+ P + +AV+ Sbjct: 142 ANPANPLAHYNRTAPEILQQHPNCKWLFV-GAGTTGTLIGCARYLREKAPEVKLIAVDTV 200 Query: 206 ASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIITVGNEDALNVARRLAREEGLLVGI 265 S K I G+G P +L++DLV+ I V + + + R +A++ GLL+G Sbjct: 201 GSINFQEVPK-KRLIPGLGTSRRPEILERDLVEHIEFVDEVETIRMCRSVAQDYGLLLGG 259 Query: 266 SSGAATVAALQVARRPENAGKLIVVVLPDFGERYLST 302 S+G VA ++ R+ AG +VV+ PD GERYL T Sbjct: 260 STGTVLVAVKRL-RKQIPAGDEVVVISPDMGERYLET 295 Lambda K H 0.318 0.136 0.383 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: 213 Number of extensions: 8 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: 310 Length of database: 317 Length adjustment: 27 Effective length of query: 283 Effective length of database: 290 Effective search space: 82070 Effective search space used: 82070 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: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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