Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_035240746.1 Q366_RS15935 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000745975.1:WP_035240746.1 Length = 544 Score = 208 bits (530), Expect = 3e-58 Identities = 161/514 (31%), Positives = 258/514 (50%), Gaps = 37/514 (7%) Query: 4 RVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGE---FEAVRA 60 +V ++DTTLRDG Q + + +K++IA +LD+ G+ IE G+P ++ G F+ VR Sbjct: 9 KVLLYDTTLRDGMQGENIFFSPGDKLKIAMRLDDAGIHYIEGGWPGSNPGAQAFFDLVRD 68 Query: 61 IAGEELDAEICGL-------ARCVK-GDIDAAIDADVDCVHVFIATSDIHLRYKLEMSRE 112 ++ A+IC + C K +I A ID+ V +F + D+H+ + +RE Sbjct: 69 TPFKQ--AKICAFGSTRRQNSTCEKDSNIKALIDSGAPVVTIFGKSWDLHVSDIMNNTRE 126 Query: 113 EALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVG 169 E L E V Y G V + AE D + + + LE A ++ G + + DT G Sbjct: 127 ENLAMITESVSYLKARGREVLYDAEHFYDGYKANPGFALETLGAALKGGTRCLVLCDTNG 186 Query: 170 VMTPPEMYRLTAEVV----DAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIG 225 P ++ +T E + D DV VH HND MAVAN++ AV AGA V TVNG G Sbjct: 187 GCLPCDIDTITRETIAHFKDYEDVIFGVHTHNDCAMAVANAINAVHAGAIMVQGTVNGYG 246 Query: 226 ERAGNASLEQVV--MALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFA 283 ER GNA L ++ +ALK + L LSR V + + P VG +AF Sbjct: 247 ERCGNADLTALIPILALKMNRACISEKNLAKLQNLSRFVSETANMPPVASRPFVGRSAFT 306 Query: 284 HESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEV--TEEQL 341 H+ G+H ++K YE + PE VG+RRR+++ + +G+ I K +E+G+++ E + Sbjct: 307 HKGGVHVSAIMKNPRAYEHMSPEFVGNRRRVLVSEQSGKSNITYKAKELGVDLGSDESKK 366 Query: 342 DEIVRRVKELGDKGKRVTEDDLEAIARDVVGEVPES-EAAVKLEEI-AVMTGNKFTPT-- 397 IV +KE+ + G D E + ++ + E ++ LE V+ +K P Sbjct: 367 SLIVNNIKEMENYGYEF--DTAEGSLKLIMERLTEQYQSHFDLESFRVVVEKDKERPCYS 424 Query: 398 -ASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEEL---GMDVELKEYRLEAITG--GT 451 A +++ + E ++ G G V A ALR+A+ + D+ L ++++ I G GT Sbjct: 425 HAMIKIRVGNETEITSAEGDGPVSALDNALRKALTAMYPGVKDLHLVDFKVRVIDGSDGT 484 Query: 452 DALAEVTVRLEDEDGNVTTARGAAEDIVMASVKA 485 DA V + D D N+ + G + DI+ AS +A Sbjct: 485 DARVRVLIESRDRD-NIFSTVGVSADIIEASWQA 517 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: 495 Number of extensions: 25 Number of successful extensions: 4 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: 544 Length adjustment: 35 Effective length of query: 464 Effective length of database: 509 Effective search space: 236176 Effective search space used: 236176 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