Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate 3608293 Dshi_1696 2-isopropylmalate synthase/homocitrate synthase family protein (RefSeq)
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__Dino:3608293 Length = 545 Score = 211 bits (537), Expect = 5e-59 Identities = 168/529 (31%), Positives = 258/529 (48%), Gaps = 40/529 (7%) Query: 1 MPDRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVAS--EGEFEAV 58 M +R+ ++DTTLRDG+QT GV + EK +IA LD G+D IE G+P A+ + EF A Sbjct: 1 MNERLYLYDTTLRDGQQTQGVQFSTPEKQQIAAALDALGIDFIEGGWPGANPTDSEFFAS 60 Query: 59 RAIAGEELDAEI-----CGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREE 113 A G + + A ++A V + + + H+ L +S E Sbjct: 61 APTFDHARFAAFGMTKRAGFSAENDDVLAAVLNAGTQAVCLVGKSHEYHVTRALGISLAE 120 Query: 114 ALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGV 170 E V + G F AE D + Y +E +A +EAGA V + DT G Sbjct: 121 NTENIARSVAHLVAQGREAIFDAEHFFDGYLANPGYAVETLQAALEAGARWVVLCDTNGG 180 Query: 171 MTPPEMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGER 227 P E+ R+TAEV+ A VP + +H HND G AVAN+LAA++AGA QV T+NG+GER Sbjct: 181 RLPAEVGRITAEVI-AAGVPGDRLGIHTHNDTGNAVANALAAIDAGARQVQGTLNGLGER 239 Query: 228 AGNASLEQVV--MALKALYDIELDVRTEM-----LVELSRLVERLTGVVVPPNTPIVGEN 280 GNA+L ++ + LK Y + LV +SR ++ + V + P VG + Sbjct: 240 CGNANLVTLIPTLLLKEPYASRFETGVSAAALRDLVRVSRTLDDILNRVPTKSAPYVGAS 299 Query: 281 AFAHESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVT--E 338 AFAH++G+H+ ++K TYE I PE VG+ R I + AG+ ++K+L + GI V + Sbjct: 300 AFAHKAGLHASAILKDPSTYEHIPPEAVGNARVIPMSNQAGQSNLRKRLADAGIAVQKGD 359 Query: 339 EQLDEIVRRVKELGDKGKRV--TEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTP 396 +L ++ VK D G + E +AR + +PE + NK+ Sbjct: 360 MRLGALLDEVKRREDMGYSFDSAQASFELLARRHLEGLPEFFEVKRYRVTVERRKNKYDR 419 Query: 397 TAS----VRVYLDGEEH----EAASTGVGSVDAAIRALREAI-EELG------MDVELKE 441 S V V G+E + G + AL +A+ ++LG D+ L + Sbjct: 420 MVSLSEAVVVLKIGDEKMLSVSESMDETGCDRGPVNALAKALGKDLGPYTPYIADLRLVD 479 Query: 442 YRLEAITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490 +++ GGT+A+ V + ED G + G + +IV AS +A V + Sbjct: 480 FKVRITNGGTEAVTRVLIDSEDGQGRRWSTVGVSANIVDASFEALVEAI 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: 577 Number of extensions: 25 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: 545 Length adjustment: 35 Effective length of query: 464 Effective length of database: 510 Effective search space: 236640 Effective search space used: 236640 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