Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate H281DRAFT_06209 H281DRAFT_06209 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= BRENDA::Q05957 (318 letters) >FitnessBrowser__Burk376:H281DRAFT_06209 Length = 290 Score = 204 bits (520), Expect = 2e-57 Identities = 104/282 (36%), Positives = 169/282 (59%), Gaps = 1/282 (0%) Query: 31 MHRLIEEHGSVLMPGVQDALSAAVVEKTGFHAAFVSGYSVSAAMLGLPDFGLLTTTEVVE 90 + R ++ ++L+PGV +AL+A + E+ G+ A FV+G ++ + LG PD GL T TEV Sbjct: 9 LRRTLQPSAALLLPGVSNALAARIAEEAGYAAVFVTGAGIANSYLGAPDIGLTTVTEVGA 68 Query: 91 ATRRITAAAPNLCVVVDGDTGGGGPLNVQRFIRELISAGAKGVFLEDQVWPKKCGHMRGK 150 I A ++ ++ D DTG G LNV R +R AGA + LEDQ +PK+CGH GK Sbjct: 69 HINAIREAV-SIPIIADADTGFGNALNVMRTVRLFERAGANCIMLEDQTFPKRCGHFEGK 127 Query: 151 AVVPAEEHALKIAAAREAIGDSDFFLVARTDARAPHGLEEGIRRANLYKEAGADATFVEA 210 AVV EE KI AA +A ++D ++ARTD+RA G E + R Y++AGAD FVEA Sbjct: 128 AVVSIEEMTAKIKAAVDARANADTLIMARTDSRAIEGFERSLERIRTYRDAGADVLFVEA 187 Query: 211 PANVDELKEVSAKTKGLRIANMIEGGKTPLHTPEEFKEMGFHLIAHSLTAVYATARALVN 270 P++++EL + + G+++ NM+ GGKTPL + E+G+ + ++ A+ A A+ N Sbjct: 188 PSSLEELARIPREAPGVQVCNMVIGGKTPLLPQAQLSELGYAGVIYANAALQAAMFAMKN 247 Query: 271 IMKILKEKGTTRDDLDQMATFSEFNELISLESWYEMESKFKN 312 +++ L+ G+ DQ+ +F+E ++++ + + + N Sbjct: 248 VLEHLRSHGSIEGREDQIMSFAERQKMVNFARYDALAKQCAN 289 Lambda K H 0.316 0.131 0.373 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: 184 Number of extensions: 7 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: 318 Length of database: 290 Length adjustment: 27 Effective length of query: 291 Effective length of database: 263 Effective search space: 76533 Effective search space used: 76533 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 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