Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_012282605.1 HM1_RS06910 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000019165.1:WP_012282605.1 Length = 531 Score = 224 bits (571), Expect = 6e-63 Identities = 162/511 (31%), Positives = 262/511 (51%), Gaps = 29/511 (5%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAV-RAI 61 DRV I+DTTLRDG Q G+SL+VE+KV+IA +LD+ GV IE G+P ++ + E RA Sbjct: 2 DRVFIYDTTLRDGTQGEGISLSVEDKVKIAARLDQLGVAYIEGGWPGSNPKDMEFFQRAQ 61 Query: 62 AGEELDAEIC--------GLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREE 113 A+I G C ++ A I++ V +F + D H+ L + EE Sbjct: 62 QMTWKHAKIAAFGSTCRPGSEACDDPNLRALIESGAPVVTIFGKSWDFHVTAALRTTLEE 121 Query: 114 ALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGV 170 L + + + + G V F AE D + + Y EV +AGAD + + DT G Sbjct: 122 NLRLVRDSITFLKNQGREVIFDAEHFYDGYKGNPAYAKEVVMTAEKAGADWIVLCDTNGG 181 Query: 171 MTPPEMYRLTAEVVDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGN 230 P ++ +T E+V + PV VH HND +AVANS+ V AGA QV T+NG GER GN Sbjct: 182 TLPHDVLSITQEMVFTLRAPVGVHVHNDGDLAVANSIMGVMAGARQVQGTMNGYGERCGN 241 Query: 231 ASLEQVV--MALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGI 288 +L V+ + LK + + + + L + + V + + + + P VG +AFAH+ GI Sbjct: 242 VNLCSVIPNLQLKMKMECLPEGKLQTLTDAAHFVGEIANMPLRNDMPFVGHSAFAHKGGI 301 Query: 289 HSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLD--EIVR 346 H ++K TYE I+PE VG+ RR+++ + +G + K +E+G++V + D +I+ Sbjct: 302 HVSALMKDPGTYEHIQPEAVGNHRRVLVSELSGMSNVIYKAKELGLDVNRQNADTKQIIE 361 Query: 347 RVKELGDKGKRV--TEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNK----FTPTASV 400 ++K L +G + E E + R GE P L+ I ++ + FT A + Sbjct: 362 QIKNLEHQGFQFEGAEASFEVLLRRAFGEDP---VPFVLDSIRLIIEKRSDADFTSEAMI 418 Query: 401 RVYLDGEEHEAASTGVGSVDAAIRALREAI---EELGMDVELKEYRLEAITGGTDALAEV 457 ++ + + A+ G G V+A ALR+A+ + L +Y++ + G A+V Sbjct: 419 KLRVGDQVVHTAAEGNGPVNAVDNALRKALLSHYPFLAECHLTDYKVRVLDGKDATEAKV 478 Query: 458 TVRLEDEDGNVTTAR-GAAEDIVMASVKAFV 487 V +E D + G + +I+ AS +A + Sbjct: 479 RVLIETRDSHDAWGTVGVSTNIIEASWQALM 509 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: 517 Number of extensions: 22 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: 499 Length of database: 531 Length adjustment: 35 Effective length of query: 464 Effective length of database: 496 Effective search space: 230144 Effective search space used: 230144 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 10 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