Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_037572568.1 BS73_RS14685 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000744815.1:WP_037572568.1 Length = 533 Score = 209 bits (532), Expect = 2e-58 Identities = 162/511 (31%), Positives = 252/511 (49%), Gaps = 31/511 (6%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62 D +FDTTLRDG Q G+ LTV +K+ IAR LDEFGV IE G+P A+ + E A Sbjct: 8 DAFHVFDTTLRDGAQREGIKLTVADKLTIARHLDEFGVGFIEGGWPGANPRDTEFFSR-A 66 Query: 63 GEELDAEIC-----GLARCVKG------DIDAAIDADVDCVHVFIATSDIHLRYKLEMSR 111 ELD G R G + A +D+ V + + D H+ L + Sbjct: 67 ATELDLSHAQLVAFGSTRRANGTAAEDQQLKALLDSGAPVVTLVAKSHDRHVELALRTTL 126 Query: 112 EEALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTV 168 +E L + VE+ G V E D R +R+Y L V + EAGAD V + DT Sbjct: 127 DENLAMVRDSVEFLRAQGRRVFIDCEHYFDGYRANREYALSVVRTAHEAGADVVVLCDTN 186 Query: 169 GVMTPPEMYRLTAEVVDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERA 228 G M P + + A+ + + +H +D G AVAN+LAAVE GA V T NG GER Sbjct: 187 GGMLPSGVREIVADTLAETGARLGIHAQDDTGCAVANTLAAVEGGATHVQCTANGYGERV 246 Query: 229 GNASLEQVVMALKALYDIELDVRTEMLVELSRLVERLTGVV-VPPNT--PIVGENAFAHE 285 GNA+L V AL+ + + L E++R+ + VV + P T P VG +AFAH+ Sbjct: 247 GNANLFPVTAALELKLGRSV-LPAGRLAEMTRISHAIAEVVNLAPATHQPYVGVSAFAHK 305 Query: 286 SGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVT--EEQLDE 343 G+H+ + + Y+ I PE VG+ R+++ AGR +++ K +E+G +++ E + Sbjct: 306 GGLHASAIKVDPDLYQHIDPELVGNTMRMLVSDMAGRASVELKGKELGFDLSGDRELVGR 365 Query: 344 IVRRVKELGDKG--KRVTEDDLEAIARDVVGEVPESEAAVKLEEIAV--MTGNKFTPTAS 399 +V +KE + G + E + R+ G++P+ A++ V + A+ Sbjct: 366 VVDVLKERENAGYTYEAADASFELLLREQSGDLPQRFFALESWRAIVEQRPDGEQANEAT 425 Query: 400 VRVYLDGEEHEAASTGVGSVDAAIRALREAIEELGMDV---ELKEYRLEAI--TGGTDAL 454 V+++ GE G G V+A RALR +E + + EL +Y++ + GT+++ Sbjct: 426 VKLWAKGERLVTTGEGNGPVNALDRALRAGLERIYPQLAAFELVDYKVRILEERHGTESV 485 Query: 455 AEVTVRLEDEDGNVTTARGAAEDIVMASVKA 485 V V D +T G +++ AS +A Sbjct: 486 TRVLVTTSDGKSEWSTV-GVGSNVIAASWQA 515 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: 571 Number of extensions: 26 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: 533 Length adjustment: 35 Effective length of query: 464 Effective length of database: 498 Effective search space: 231072 Effective search space used: 231072 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 Jul 26 2024. The underlying query database was built on Jul 25 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