Align 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_093393959.1 BM091_RS05055 alpha-isopropylmalate synthase regulatory domain-containing protein
Query= curated2:Q2LWJ3 (516 letters) >NCBI__GCF_900114975.1:WP_093393959.1 Length = 518 Score = 355 bits (910), Expect = e-102 Identities = 194/498 (38%), Positives = 301/498 (60%), Gaps = 3/498 (0%) Query: 6 KRIYIFDTTLRDGEQSPGSSMNPAEKLRIARQLEKMGVDIIEAGFPIASEGDFLSVQQIA 65 K + DTTLRDG + PG + P EK++IARQ+ +GVDI+E GFP ASE + ++ +A Sbjct: 2 KHVAFLDTTLRDGIKIPGLMLLPEEKIQIARQIATLGVDILEGGFPAASEEQYRTLCVMA 61 Query: 66 QEIRGAQIAGLARANNADIDR-AWEAIRDAANPRIHTFISSSDIHLKYQLRKSREQVLKE 124 +EI+G LARA N + R A + ++ PRIHTFI +S + + L+K ++ L+ Sbjct: 62 EEIQGPSFCVLARATNPEDFRIARDVLKRHPKPRIHTFIPASAAYRDHFLKKPLDECLRI 121 Query: 125 AVAAVERARSYTPNVEFSPMDATRTDRGYLCEMVEAVIAAGASTVNIPDTVGYAIPQEFG 184 AV AV+R + +VEFS +DA R L ++++AV+ AGA T+ DTVGYA P Sbjct: 122 AVEAVKRGKDVADHVEFSFVDAFRASENELLKLLDAVLEAGADTITFADTVGYATPWLIE 181 Query: 185 ELIAYLRANVPNISQAIISVHCHNDLGLAVANSLSAILNGARQVECTINGIGERAGNTAM 244 +I + + + + + ++ +HCHNDLGLA NS++A+ GA V CT+NG+GERAGN + Sbjct: 182 NIIGKICSEIKD--EIVVGIHCHNDLGLATPNSIAALRAGASLVHCTVNGLGERAGNARL 239 Query: 245 EEVVMALRTRKDLFGFYTGIKTESIYQSSRLLTQITGVAVQPNKAIVGANAFAHESGIHQ 304 EE+ + G T + + I RLL + TG++ P K + G+ AF E Q Sbjct: 240 EEIATIIAIHGKALGLSTSVAMDRIGPVCRLLERHTGISFGPLKPLTGSYAFYCEPSGPQ 299 Query: 305 DGLIKEKITYEIMTPQSVGISDSHIVLGKHSGRHAVSEHLKKLGFNLSDTELNKIFVRFK 364 G + E ++ + +G+ + + + + +K+LG+ L + E + + F+ Sbjct: 300 IGDVAELPPCFVIREEDIGMVKNGEPMDQDTPFEVFKARVKELGYVLKEGEYQRCYETFQ 359 Query: 365 ELADAKKNVFDEDLEAIVYEELYRVEDKYKLIYLNVVSGNVAIPTATMQMEVDREIVQDA 424 LA K+N+F+ DLE IV + L+ V KY+L+YLNV +G++ +P AT+Q+E+D ++VQDA Sbjct: 360 RLASKKENIFNSDLELIVRQALFHVPQKYRLLYLNVSAGSIPVPHATVQLEIDGQVVQDA 419 Query: 425 GFGVGPVDATFDAIRKITGTNYDLLRYVVNAISGGTDAQGEVTVQLKFNGRSVVGHGADL 484 GFG GPVDA F I ++ L+ Y V A + GTDAQG V ++++ V G GA + Sbjct: 420 GFGHGPVDAAFKTIFRMVRRFPKLIHYEVKAATLGTDAQGMVLLRVQEGDTIVDGWGAHV 479 Query: 485 DVIVASARAYINALNRLE 502 D+++ASA+A I+ALN+LE Sbjct: 480 DIVLASAQALIDALNKLE 497 Lambda K H 0.317 0.134 0.371 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: 590 Number of extensions: 17 Number of successful extensions: 3 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: 516 Length of database: 518 Length adjustment: 35 Effective length of query: 481 Effective length of database: 483 Effective search space: 232323 Effective search space used: 232323 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 (21.7 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