Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate NP_661512.1 CT0612 alpha-isopropylmalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000006985.1:NP_661512.1 Length = 534 Score = 222 bits (566), Expect = 2e-62 Identities = 162/524 (30%), Positives = 263/524 (50%), Gaps = 51/524 (9%) Query: 5 VRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFE-------- 56 + ++DTTLRDG Q ++L+V++K+ IA +LDEFGVD IE G+P ++ + E Sbjct: 3 IELYDTTLRDGTQGEHINLSVQDKLLIAERLDEFGVDFIEGGWPSSNPKDEEFFLKARKL 62 Query: 57 ------------AVRAIAGEELDAEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLR 104 R++ E D + GL RC + + +F T H Sbjct: 63 NLKHARLTAFGSTARSLDNVENDPNLVGLVRC-----------EAPVLTIFGKTWKAHSV 111 Query: 105 YKLEMSREEALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADR 161 L +S +E E V++ + G V F AE D + + + + A V+ GA R Sbjct: 112 KSLGISDDENAELIYRSVKFLVESGREVFFDAEHFFDGWKDNAGFAERMIAAAVDGGASR 171 Query: 162 VNVPDTVGVMTPPEMYRLTAEVVDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTV 221 V + DT G P E+ + V + + V V +H HND +AVANS+ AV AGA QV T+ Sbjct: 172 VVLCDTNGGTLPHEIAAIVTRVREIIGVSVGIHAHNDSDLAVANSIEAVRAGATQVQGTI 231 Query: 222 NGIGERAGNASLEQVV----MALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIV 277 NGIGER GNA+L ++ + L A + D+++ L +S+ V + + P V Sbjct: 232 NGIGERCGNANLVSIIPNLMLKLGAEFSHVQDLKS--LTSMSKFVYEILNLPPDSKAPFV 289 Query: 278 GENAFAHESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVT 337 G++AFAH+ GIH V+K++ YE I P VG+R+R+++ + AG+ I+ K +E+GI + Sbjct: 290 GKSAFAHKGGIHVSAVMKESSLYEHIDPMLVGNRQRVLVSELAGQSNIRYKAQELGISLP 349 Query: 338 E--EQLDEIVRRVKELGDKGKRV--TEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGN- 392 E E +V VK+L +G + E E I R +G+ + V ++ + G Sbjct: 350 EKGEVFKNLVNHVKKLEHQGYQFDGAEASFELILRRELGQF-KPYFEVLESKVVIQNGQE 408 Query: 393 -KFTPTASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEELGMD---VELKEYRLEAIT 448 K A ++V + E + + G G V+A +ALR+A+ D + L +Y++ + Sbjct: 409 IKAVDQAVMKVMVGDETEQTVADGDGPVNALDKALRKALLHFYPDIRMIRLIDYKVRVLE 468 Query: 449 GGTDALAEVTVRLEDEDG-NVTTARGAAEDIVMASVKAFVRGVN 491 + A+V V +E DG N G + +I+ AS++A +N Sbjct: 469 EKSGTSAKVRVLIESSDGQNSWGTVGVSTNIIEASLQALNDSIN 512 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: 511 Number of extensions: 21 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: 534 Length adjustment: 35 Effective length of query: 464 Effective length of database: 499 Effective search space: 231536 Effective search space used: 231536 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