Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_012566191.1 RC1_RS04635 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000016185.1:WP_012566191.1 Length = 547 Score = 220 bits (561), Expect = 9e-62 Identities = 168/520 (32%), Positives = 261/520 (50%), Gaps = 37/520 (7%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGE---FEAVR 59 +RV ++DTTLRDG QT GV V +K+ IAR+LD G+D +E G+P A+ + F A Sbjct: 5 NRVYLYDTTLRDGAQTSGVDFGVADKIAIARELDALGIDYVEGGWPGANPTDDAFFAAPP 64 Query: 60 AIAGEELDA----EICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEAL 115 A+A A G + G + A +++ V + + D H+ L +SR E L Sbjct: 65 ALARATFTAFGMTRRPGRSAANDGGLAALLNSGAPAVCIVGKSWDFHVDVALGISRTENL 124 Query: 116 ERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMT 172 E + V G F AE D R + ++ L +A EAGA + + DT G Sbjct: 125 ELIRDSVAAIVARGREALFDAEHFFDGYRRNPEFALSCVQAAHEAGARWIVLCDTNGGTL 184 Query: 173 PPEMYRLTAEVVDAVDVP-VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNA 231 P E+ R+ AEV ++ + +HCHND AVANSLAAV AGA + T+NG+GER GNA Sbjct: 185 PHEIERIVAEVARSIPGGRLGIHCHNDTENAVANSLAAVRAGARMIQGTLNGLGERCGNA 244 Query: 232 SLEQVVMALKALYDIELDVRT---EMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGI 288 +L ++ L E V + LV +SR+++ + P VGE+AFAH+ G+ Sbjct: 245 NLVSLLPTLMLKLGYETGVARADLKRLVHVSRMLDERMNRAPNRHAPYVGESAFAHKGGL 304 Query: 289 HSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVT--EEQLDEIVR 346 H V K YE I P+ VG+RR I++ AGR + +L E+G+EV + ++ ++V Sbjct: 305 HVSAVEKDPACYEHIDPDLVGNRRHILVSDQAGRSNVLARLREVGLEVDPGDGRIGQLVE 364 Query: 347 RVKELGDKGKRV--TEDDLEAIARDVVGEVPESEAAVK---LEEIAVMTGNKFTPTASVR 401 VK +G E E +AR +G+VP+ V L+E N+ + Sbjct: 365 AVKRREYEGYAYDGAEASFELLARRALGQVPDFFRLVSFRVLDERRWNARNELVTLSEAT 424 Query: 402 VYLD-----------GEEHEAASTGVGSVDAAIRALREAIEELGMDVE---LKEYRLEAI 447 V ++ G+ + G G V+A +ALR+A+ ++ +E L +Y++ + Sbjct: 425 VKVEVPPFAQVGTAPGQPVMTVAEGNGPVNALDQALRKALRDVYPQLEGMRLVDYKVRIL 484 Query: 448 T--GGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKA 485 T GT A+ V + +D G+ + G + +I+ AS A Sbjct: 485 TPNDGTKAVTRVMIETQDRSGDRWSTVGVSANIIDASFNA 524 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: 579 Number of extensions: 19 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: 547 Length adjustment: 35 Effective length of query: 464 Effective length of database: 512 Effective search space: 237568 Effective search space used: 237568 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