Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_193589535.1 MA_RS19760 2-isopropylmalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000007345.1:WP_193589535.1 Length = 495 Score = 488 bits (1255), Expect = e-142 Identities = 244/493 (49%), Positives = 342/493 (69%), Gaps = 3/493 (0%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62 + + DTTLRDGEQTPGV+LT E+K+ IAR LDE ++ IEAG + S GE E+++A+A Sbjct: 4 ENIHFLDTTLRDGEQTPGVALTREKKLLIARALDEMRINVIEAGSAITSAGERESIKAVA 63 Query: 63 GEELDAEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALERAIEGV 122 LDAEIC R VK D+D A++ DVD +H+ SD+H++ K++ R+ + A E Sbjct: 64 NAGLDAEICSYCRIVKMDVDHALECDVDSIHLVAPVSDLHIKTKIKKDRDTVRQIAAEVT 123 Query: 123 EYASDHGVTVEFSAEDATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPPEMYRLTAE 182 EYA DHG+ VE S EDA+R D ++L +Y ++AGADR+ DTVG++ P + + + Sbjct: 124 EYAKDHGLIVELSGEDASRADPEFLKAIYSDGIDAGADRLCFCDTVGLLVPEKTTEIFRD 183 Query: 183 VVDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNASLEQVVMALKA 242 + ++ P+S+HCHNDFG+A AN++AA+ AGA+Q HVT+NG+GERAGNASLE+VVM+L+ Sbjct: 184 LSSSLKAPISIHCHNDFGLATANTVAALAAGAKQSHVTINGLGERAGNASLEEVVMSLEW 243 Query: 243 LYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHGVIKKAETYEP 302 LY + ++ E + SRLV RLTG+ V PN +VG NAF HE+GIH HG++ TYEP Sbjct: 244 LYKYDTGIKHEQIYRTSRLVSRLTGIPVSPNKALVGGNAFTHEAGIHVHGLLADKSTYEP 303 Query: 303 IRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLDEIVRRVKELGDKGKRVTEDD 362 + PE +G +R+IVLGKHAGR +I L+EMG+E E Q +EI RVK++GD+GK +T+ D Sbjct: 304 MSPEYIGRQRQIVLGKHAGRSSITLALKEMGLEADEAQTEEIFNRVKQMGDQGKHITDAD 363 Query: 363 LEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTASVRVYLDGEEHEAASTGVGSVDAA 422 L+ IA V+ E VKLEE +++GN+ TPTAS+++ + +E A G G VDA Sbjct: 364 LQTIAETVLDIY--KEPIVKLEEFTIVSGNRVTPTASIKLNVKDKEIVQAGIGNGPVDAV 421 Query: 423 IRALREAIEELGMDVELKEYRLEAITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMAS 482 I A+R A+ DV L+EY +++ITGGTDAL EV V+L ++G V TA GA DI+MAS Sbjct: 422 INAIRRAVSSCAEDVVLEEYHVDSITGGTDALVEVRVKL-SKNGKVITASGARTDIIMAS 480 Query: 483 VKAFVRGVNRLAR 495 V+A + G+NRL R Sbjct: 481 VEAVMNGMNRLIR 493 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: 660 Number of extensions: 28 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: 495 Length adjustment: 34 Effective length of query: 465 Effective length of database: 461 Effective search space: 214365 Effective search space used: 214365 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