Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_013645641.1 METBO_RS10235 homocitrate synthase family protein
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000191585.1:WP_013645641.1 Length = 391 Score = 385 bits (988), Expect = e-111 Identities = 191/371 (51%), Positives = 266/371 (71%) Query: 2 PDRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAI 61 P+++ ++DTTLRDGEQTPGV L EK++IA+KLDE G+ IEAGFPV S+ E ++V AI Sbjct: 17 PEKITVYDTTLRDGEQTPGVCLRTPEKLKIAKKLDEVGIHQIEAGFPVVSKEEKKSVTAI 76 Query: 62 AGEELDAEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALERAIEG 121 E+L+A+I L+R K DID AID DVD + F++TSD+HL++K++MSREE L + Sbjct: 77 VNEDLNAQILCLSRTKKSDIDTAIDCDVDGIITFMSTSDLHLKHKIKMSREEILNVCMNS 136 Query: 122 VEYASDHGVTVEFSAEDATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPPEMYRLTA 181 +E+A DHG+ V FSAEDATRTD D+L ++YK + G DRV++ DTVG ++P M L Sbjct: 137 IEHAKDHGLFVAFSAEDATRTDLDFLKKMYKKADDYGVDRVHIADTVGAISPYGMDYLVK 196 Query: 182 EVVDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNASLEQVVMALK 241 ++ ++ +++HCHNDFGMA+ANS+A + AGA V TVNGIGERAGNA+LE++VM LK Sbjct: 197 QLRSTINAEIALHCHNDFGMALANSIAGLLAGANAVSTTVNGIGERAGNAALEELVMTLK 256 Query: 242 ALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHGVIKKAETYE 301 +Y ++L ELS+LVE LT + +P N PIVG+N F HESGIH VI++ TYE Sbjct: 257 FIYGVDLGFDVSKFCELSKLVESLTHMDIPYNKPIVGKNIFRHESGIHVDAVIEEPLTYE 316 Query: 302 PIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLDEIVRRVKELGDKGKRVTED 361 P PE +GHRR+IVLGKH+G A++ KL E GI+VT+++L +IV +VK ++G + ++ Sbjct: 317 PFLPELIGHRRQIVLGKHSGCRAVRAKLNECGIDVTKDELCKIVEQVKSKREEGNYINDE 376 Query: 362 DLEAIARDVVG 372 +I V G Sbjct: 377 LFNSIVASVRG 387 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: 482 Number of extensions: 18 Number of successful extensions: 1 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: 391 Length adjustment: 32 Effective length of query: 467 Effective length of database: 359 Effective search space: 167653 Effective search space used: 167653 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: 51 (24.3 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