Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_026608178.1 METAC_RS0118650 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000427445.1:WP_026608178.1 Length = 531 Score = 231 bits (588), Expect = 6e-65 Identities = 178/525 (33%), Positives = 265/525 (50%), Gaps = 44/525 (8%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVAS--EGEFEAVRA 60 +R+ +FDTTLRDG QT GV ++ +K IA LD G+D IE G+P A+ + EF A R Sbjct: 4 ERLYLFDTTLRDGAQTTGVDFSLADKRHIAAMLDSLGLDYIEGGYPGANPLDTEFFASRP 63 Query: 61 IAGEELDAEICGLARCVKG-----DIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEAL 115 A R + + + + AD D + D + L + EE L Sbjct: 64 KLHHARFAAFGMTKRAGRSAGNDPGVASLLAADADSITYVAKAWDYQVHVALGCTLEENL 123 Query: 116 ERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMT 172 E ++ +E A G E D + + DY L+ KA EAGA + + DT G Sbjct: 124 ESIVQSIEAARSKGREALLDCEHFFDGFKANPDYALQCAKAAYEAGARWIVLCDTNGGTL 183 Query: 173 PPEMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAG 229 P E+ R+ AE A+ VP + VH HND AVANSLAAV AGA Q+ T+NG+GER G Sbjct: 184 PHEIERIVAEA--ALHVPGAHLGVHAHNDTENAVANSLAAVRAGARQIQGTLNGLGERCG 241 Query: 230 NASLEQVVMALKALYDI----ELDVRTEMLVELSRLVERLTGVVV-PPN--TPIVGENAF 282 NA+L ++ L D E+ V E L L+++ L ++ PN P VG +AF Sbjct: 242 NANLVSLIPTLLLKPDFAEHFEIGVPFEKLASLTKISHTLDELLNRAPNRHAPYVGASAF 301 Query: 283 AHESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLD 342 A ++GIH+ V+K TYE + PE VG++RR+++ AG+ I +LE +G+ +LD Sbjct: 302 ATKAGIHASAVMKAPRTYEHVAPESVGNKRRLLVSDQAGKSNILAELERIGV-----RLD 356 Query: 343 EIVRRVKELGDKGKRV---------TEDDLEAIARDVVGEVPE----SEAAVKLEEIAVM 389 + RRV L ++ K+ + E +AR +GE P V +E Sbjct: 357 KDDRRVTTLLEEVKQKEALGYAYEGADASFELLARRALGEAPTYFEVERFRVDVERRHNA 416 Query: 390 TGNKFTPT-ASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEELGM---DVELKEYRLE 445 G+ T + A+V+V +DGE +A+ G G V+A ALR+ + + D+EL +YR+ Sbjct: 417 QGDLVTVSEATVKVRVDGEVLISAAEGEGPVNALDLALRKDLGKYQRYIGDLELVDYRVR 476 Query: 446 AITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490 GGTDA+ V + D G + G + +I+ AS +A + Sbjct: 477 VFQGGTDAVTRVLIEFRDAGGESWSTVGVSANIIDASFQALTDAI 521 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: 563 Number of extensions: 26 Number of successful extensions: 5 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