Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_085635863.1 MGEO_RS06350 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_002115805.1:WP_085635863.1 Length = 539 Score = 212 bits (539), Expect = 3e-59 Identities = 166/525 (31%), Positives = 260/525 (49%), Gaps = 39/525 (7%) Query: 4 RVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIAG 63 R+ ++DTTLRDG+QT GV + EK I LD G+D IE G+P A+ + + Sbjct: 5 RLTLYDTTLRDGQQTQGVQFSTPEKHRIVEALDALGIDYIEGGWPGANPTDSAFFDEVGH 64 Query: 64 EELDAEICGLA----RCVKGD--IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALER 117 G+ R + D + A ++A V + T D H+ L ++ EE +E Sbjct: 65 TRATVTAFGMTKRAGRSAENDDVLAAVMNAGTKSVCLVGKTHDFHVTAALGITLEENVEH 124 Query: 118 AIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPP 174 V + F AE D + + DY L A EAGA + + DT G P Sbjct: 125 IRASVAHIVSQKREALFDAEHFFDGYKANPDYALTCLHAAYEAGARWIVLCDTNGGALPS 184 Query: 175 EMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNA 231 E+ R+T E V A +P V +H HND MAVA +LAAV+AGA Q+ T+NG+GER GNA Sbjct: 185 EVGRIT-EAVIASGIPGTHVGIHTHNDTEMAVATTLAAVDAGARQIQGTLNGLGERCGNA 243 Query: 232 SLEQVV--MALKALY--DIELDVRTEML---VELSRLVERLTGVVVPPNTPIVGENAFAH 284 +L ++ + LK Y E V E L +SR+++ + V + VG +AFAH Sbjct: 244 NLTSLIPTLLLKEPYASTYETGVTLEALEGMTRISRMLDEILNRVPLKQSAYVGSSAFAH 303 Query: 285 ESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQ--LD 342 ++G+H+ ++K TYE I P VG+RR I + AG+ ++++L E GIEV ++ L Sbjct: 304 KAGLHASAILKNPTTYEHIDPALVGNRRVIPMSNQAGQSNLRRRLAEAGIEVPDKDPALA 363 Query: 343 EIVRRVKELGDKGKR--VTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTAS- 399 I+ R+K +G + E +ARD +G +PE + NK+ S Sbjct: 364 RILDRIKAREAEGYSYDTAQASFELLARDELGMLPEFFEVKRYRVTVERRKNKYNKMISH 423 Query: 400 ---VRVYLDGEEHEAAST----GVGSVDAAIRALREAI-EELGM------DVELKEYRLE 445 V V G+E + + + +G+ + AL +A+ ++LG D+ L ++++ Sbjct: 424 SEAVVVVKVGDEKKLSVSESMDELGNDRGPVNALSKALAKDLGPYQHMIDDLRLVDFKVR 483 Query: 446 AITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490 GGT+A+ V + ED G + G + +I+ AS +A + V Sbjct: 484 ITQGGTEAVTRVIIDSEDGQGRRWSTVGVSANIIDASFEALLDAV 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: 622 Number of extensions: 30 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: 539 Length adjustment: 35 Effective length of query: 464 Effective length of database: 504 Effective search space: 233856 Effective search space used: 233856 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