Align 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_035240377.1 Q366_RS14820 homocitrate synthase
Query= curated2:B0TCR1 (512 letters) >NCBI__GCF_000745975.1:WP_035240377.1 Length = 557 Score = 221 bits (564), Expect = 4e-62 Identities = 180/541 (33%), Positives = 262/541 (48%), Gaps = 53/541 (9%) Query: 3 KRVVIFDTTLRDGEQSPGVSLNLHEKLEIAQQLARLGVDVIEAGFPIASPGDFEAVKAVA 62 + V IFDTTLRDGEQ GV+ KL IA+ LA GV IE GFP ++P +F+ VK +A Sbjct: 24 QEVEIFDTTLRDGEQG-GVTFKGDSKLRIARFLADTGVSTIEVGFPSSTPLEFDTVKQIA 82 Query: 63 EQVRGPVICALARANRKDIERAAEALRGAEEARIHTFIATSPIHMQHKLRMEPDKVLDTA 122 + V GP IC L + ++I+R +AL IH F + +P++ ++ A Sbjct: 83 DTVEGPHICGLTTMDFENIKRTWQALENNPNPTIHVFTLNIDEASIRAYKADPNEQIEKA 142 Query: 123 VDAVKLAKSFTSN---VEFSAED-------AFRSDVGFL----CRIFSAAIEAGATTINI 168 AV AK T VEFSA++ + + FL I+ AI+AGA INI Sbjct: 143 SRAVAYAKELTGGKGRVEFSAQNTILALSQSLNPEYSFLQEYISNIYGCAIKAGADVINI 202 Query: 169 PDTVGYATP---QEFGAFIKAIINGTPNIDKAIVSVHCHNDLGLAVANTLAALENGALQV 225 P TV QE + K ++ GT D I+S H HND G++VA+TLAA+E G QV Sbjct: 203 PHTVAKGIEIEIQEAIQYFKMLVEGT---DDVILSFHAHNDFGVSVADTLAAVEQGIRQV 259 Query: 226 EGTINGIGERAGNASLEEVIMALYTRKPFYNLE--TSINKSEIYRTSRLVSNLTGMLVQP 283 EGT +GERAGN LE+VIM L + KP YN + T+ +R + + + + Sbjct: 260 EGTWYSLGERAGNTPLEQVIMNL-SLKPSYNRKFFTAFKLERTNAVARFIERESSIPIPY 318 Query: 284 NKAIVGKNAFAHESGIHQDGVLKERTTYEIM----NPEMIGIFTNNIVLGKHSGRHAFRE 339 N +G NA H SG+H DG K + E + +PE IG N + K +G Sbjct: 319 NAPGIGPNALRHGSGVHSDGDKKGKAIGENIYLPCSPEDIGWTGNTHQITKLTGVAGVTA 378 Query: 340 RLKELGYSLDDEKLTKAFARFKALADRK-REIT--DEDLVVLVEDELRAFPEAYSLEYLH 396 RL+ELG+ + KAF R + + K R+IT D++L ++ +D + E Sbjct: 379 RLEELGFEFE-----KAFVREHIMPEIKSRDITYGDKELRMIGDDFRYTGKDHVEFEDYA 433 Query: 397 IT----SGTVLVPTATVRLRREEENFEEASCGDGPVDAAYKAIEKITGTG---ARLASYA 449 SG + + +++ E + +GP++A + AI+ + G +L Y Sbjct: 434 FNKFAKSGDRHAQVVLI-IDGKKKTSEPFTGKNGPINAVFSAIDHVLELGDKKPKLVVYE 492 Query: 450 ISATTAGEDSQGEVSVKLEREGR---------FYTGRGVDTDIIVASAKAYLNAVNKIVF 500 S S E V L G + GR D I ASAKAY+ A+++ + Sbjct: 493 PSNRGRTHSSAAEALVVLSGNGHELNYHLTAPVWVGRATHDDTITASAKAYVQALSRFMT 552 Query: 501 D 501 D Sbjct: 553 D 553 Lambda K H 0.317 0.133 0.367 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: 625 Number of extensions: 23 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 512 Length of database: 557 Length adjustment: 35 Effective length of query: 477 Effective length of database: 522 Effective search space: 248994 Effective search space used: 248994 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 (21.6 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