Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate Synpcc7942_0428 Synpcc7942_0428 putative alpha-isopropylmalate/homocitrate synthase family transferase
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__SynE:Synpcc7942_0428 Length = 542 Score = 217 bits (552), Expect = 9e-61 Identities = 163/519 (31%), Positives = 259/519 (49%), Gaps = 36/519 (6%) Query: 5 VRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIAGE 64 + ++DTTLRDG Q G+SL++E+K+ IA LD GV IE G+P A+ + + + Sbjct: 9 IAVYDTTLRDGAQREGLSLSLEDKLRIAHCLDRLGVKFIEGGWPGANPKDVQFFWELQQR 68 Query: 65 ELD-AEI---CGLARC--VKGD---IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEAL 115 L AE+ C R + G+ + A + A V +F + D+H+ L+ S +E L Sbjct: 69 PLQQAEVVAFCSTRRPGQIAGEDELLKALLAAGTTWVTIFGKSWDLHVVEGLKTSLDENL 128 Query: 116 ERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMT 172 + + Y V + AE D + DY L+ A +EAGA+ + + DT G Sbjct: 129 VMISDSIAYLRTCDRRVIYDAEHWFDGYLANPDYALQTLAAAIEAGAEWIVLCDTNGGCL 188 Query: 173 PPEMYRLTAEVVDA--------VDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGI 224 P ++ + A V+D + +H HND AVAN++AAV+AGA VH T+NG Sbjct: 189 PHQISEIVAAVLDRFPSLAPDQTGPQLGIHTHNDSETAVANAIAAVQAGARMVHGTINGY 248 Query: 225 GERAGNASLEQVV--MALKALYDIELDVRTEMLVEL---SRLVERLTGVVVPPNTPIVGE 279 GER GNA+L V+ + LK YD V TE L++L SRLV + + + VG+ Sbjct: 249 GERCGNANLCSVIPNLQLKLGYDC---VETEQLMQLTATSRLVSEIVNLAPDDHAAYVGQ 305 Query: 280 NAFAHESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEV--T 337 +AFAH+ GIH V + TYE IRPE VG+ RRIV+ + +G + K G+++ Sbjct: 306 SAFAHKGGIHVSAVERNPLTYEHIRPEQVGNLRRIVISEQSGLSNVLAKARSFGLDLQRN 365 Query: 338 EEQLDEIVRRVKELGDKGKR--VTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFT 395 + +++ R+KEL +G + E + + R+ G+ P + Sbjct: 366 DPACRDLLARLKELESQGYQFEAAEASFDLLMREATGDRPHFFDLKDFHVHCSKQRQELN 425 Query: 396 PTASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEEL---GMDVELKEYRLEAITGGTD 452 A+V+V + G + ++ G G V A ALR+AI M L +Y++ + G Sbjct: 426 ALATVKVAVTGRDILESAEGNGPVSALDAALRKAIGSFYPAVMQFHLSDYKVRILDGAAG 485 Query: 453 ALAEVTVRLEDEDGNVT-TARGAAEDIVMASVKAFVRGV 490 A+ V +E +G+ + G + +I+ AS +A V G+ Sbjct: 486 TSAKTRVLVESSNGSQRWSTVGVSGNIIEASYQAVVEGI 524 Lambda K H 0.315 0.133 0.364 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: 512 Number of extensions: 22 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: 499 Length of database: 542 Length adjustment: 35 Effective length of query: 464 Effective length of database: 507 Effective search space: 235248 Effective search space used: 235248 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 (21.5 bits) S2: 52 (24.6 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