Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate GFF1624 PGA1_c16460 2-isopropylmalate synthase/homocitrate synthase-like protein
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__Phaeo:GFF1624 Length = 543 Score = 217 bits (552), Expect = 9e-61 Identities = 166/526 (31%), Positives = 268/526 (50%), Gaps = 39/526 (7%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVAS---EGEFEAV- 58 +R+ ++DTTLRDG+QT GV + EKV+IA LD GVD IE G+P A+ G F+A Sbjct: 4 ERLYLYDTTLRDGQQTQGVQFSTTEKVQIATALDGLGVDYIEGGWPGANPTDSGFFDAAP 63 Query: 59 RAIAGEELDAEICGLARCVKGD--IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALE 116 R A R + D + A ++A V + + D H+ + L ++ EE L+ Sbjct: 64 RTRATMTAFGMTKRAGRSAENDDVLAAVLNAGTAAVCLVGKSHDYHVTHALGITLEENLD 123 Query: 117 RAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTP 173 + + G F AE D + + DY L +A +EAGA V + DT G P Sbjct: 124 NIRASIAHLVAQGREALFDAEHFFDGYKDNPDYALAACRAALEAGARWVVLCDTNGGTLP 183 Query: 174 PEMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGN 230 ++ R+ AEV+ A +P + +H HND AVA SLAAV+AGA Q+ T+NG+GER GN Sbjct: 184 GDVGRIVAEVI-AAGLPGDHLGIHTHNDTENAVACSLAAVDAGARQIQGTLNGLGERCGN 242 Query: 231 ASLEQVV--MALKALYDIELDVRTE-----MLVELSRLVERLTGVVVPPNTPIVGENAFA 283 A+L ++ + LK Y + D+ L LSR+++ + V VG +AFA Sbjct: 243 ANLTTLIPTLLLKPPYADQFDIGVSHEGLSTLTALSRMLDEILNRVPTKQAAYVGASAFA 302 Query: 284 HESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVT--EEQL 341 H++G+H+ ++K TYE I P VG+ R I + AG+ ++++L E G+ V + L Sbjct: 303 HKAGLHASAILKDPSTYEHIDPALVGNARIIPMSNQAGQSNLRRRLSEAGLRVENGDPAL 362 Query: 342 DEIVRRVKELGDKGKR--VTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTAS 399 I+ R+K +G + E +AR+ +G++P + + NK+ S Sbjct: 363 ARILERIKTREAEGYSYDTAQASFEILAREELGQLPSFFEVKRYKVTVERRKNKYDRMVS 422 Query: 400 -----VRVYLDGEEHEAASTGV---GSVDAAIRALREAI-EELGM------DVELKEYRL 444 V V +DG++ + S + GS + AL +A+ ++LG D+ L ++++ Sbjct: 423 LSEAVVVVKVDGQKLLSVSESLDETGSDRGPVNALAKALTKDLGQYSKALDDMRLVDFKV 482 Query: 445 EAITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490 GGT+A+ V + ED G + G + +I+ AS +A + + Sbjct: 483 RITQGGTEAVTRVIIDSEDGAGRRWSTVGVSANIIDASFEALLDAI 528 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: 565 Number of extensions: 24 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: 499 Length of database: 543 Length adjustment: 35 Effective length of query: 464 Effective length of database: 508 Effective search space: 235712 Effective search space used: 235712 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