Align Homocitrate synthase AksA; EC 2.3.3.14; (R)-homo(2)citrate synthase; EC 2.3.3.-; (R)-homo(3)citrate synthase; EC 2.3.3.- (uncharacterized)
to candidate Synpcc7942_0428 Synpcc7942_0428 putative alpha-isopropylmalate/homocitrate synthase family transferase
Query= curated2:Q8TW28 (397 letters) >FitnessBrowser__SynE:Synpcc7942_0428 Length = 542 Score = 179 bits (453), Expect = 2e-49 Identities = 134/400 (33%), Positives = 204/400 (51%), Gaps = 31/400 (7%) Query: 19 VIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRRIAHE 78 + VYDTTLRDG Q G+S + E KL IAH LD LGV+ IE G+P + + + Sbjct: 9 IAVYDTTLRDGAQREGLSLSLEDKLRIAHCLDRLGVKFIEGGWPGANPKDVQFFWELQQR 68 Query: 79 GLN-ADILCLARTLRGD--------VDAALDCDVDGVITFIATSELHLKHKLRMSREEVL 129 L A+++ T R + A L V F + +LH+ L+ S +E L Sbjct: 69 PLQQAEVVAFCSTRRPGQIAGEDELLKALLAAGTTWVTIFGKSWDLHVVEGLKTSLDENL 128 Query: 130 ERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVGVMI 186 I+D++ Y + V + AE DG ++ + A E GA+ + DT G + Sbjct: 129 VMISDSIAYLRTCDRRVIYDAEHWFDGYLANPDYALQTLAAAIEAGAEWIVLCDTNGGCL 188 Query: 187 PAAMRLFVAKIRE--------VVDLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGI 238 P + VA + + +G+H H+D AVAN++AAV+AGA+ + T+NG Sbjct: 189 PHQISEIVAAVLDRFPSLAPDQTGPQLGIHTHNDSETAVANAIAAVQAGARMVHGTINGY 248 Query: 239 GERAGNAALEEVIMALKELYGIDPGFNTEVLAEL---SRKVSEYSGIDVPPNKAVVGENA 295 GER GNA L VI L+ G D TE L +L SR VSE + + A VG++A Sbjct: 249 GERCGNANLCSVIPNLQLKLGYDC-VETEQLMQLTATSRLVSEIVNLAPDDHAAYVGQSA 307 Query: 296 FRHESGIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGVEPE--EE 353 F H+ GIHV+AV P TYE I P++VG R+IV+ + +G V+AK G++ + + Sbjct: 308 FAHKGGIHVSAVERNPLTYEHIRPEQVGNLRRIVISEQSGLSNVLAKARSFGLDLQRNDP 367 Query: 354 IVEEVLKRIKALGDR--RVRVTDSKLEEIVRNVLESRGDR 391 ++L R+K L + + ++ + ++R E+ GDR Sbjct: 368 ACRDLLARLKELESQGYQFEAAEASFDLLMR---EATGDR 404 Lambda K H 0.317 0.135 0.380 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: 452 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: 397 Length of database: 542 Length adjustment: 33 Effective length of query: 364 Effective length of database: 509 Effective search space: 185276 Effective search space used: 185276 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: 51 (24.3 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