Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate CA265_RS15855 CA265_RS15855 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Pedo557:CA265_RS15855 Length = 386 Score = 340 bits (872), Expect = 6e-98 Identities = 189/397 (47%), Positives = 256/397 (64%), Gaps = 17/397 (4%) Query: 18 HIPNPTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMA 77 H PN Y I DTTLRDGEQ PG + QK+E A+ L LGVD+IEAGFP +S DF + Sbjct: 3 HDPNKVY--IFDTTLRDGEQVPGCQLDTNQKVEIAKSLELLGVDVIEAGFPVSSPGDFNS 60 Query: 78 VKMIAEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEY 137 V +++ V N P+I ++R N+ DI A +AL++AKRPR+ T I +S H+++ Sbjct: 61 VIELSKAVTN--------PIICALTRANKNDIDVAADALRYAKRPRIHTGIGSSDFHIKH 112 Query: 138 KLRKSKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTI 197 K +++++LE A V++++ D++F AEDA R+D EFL ++ VI AGAT + I Sbjct: 113 KFNSTREEILERAVEAVRYSKKF-VEDVEFYAEDAGRADIEFLAKMVEAVIAAGATVVNI 171 Query: 198 PDTVGIAMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVT 257 PDT G +P +YG I +K N I+ AI++ HCHNDLGLATAN+I G + GARQ+E T Sbjct: 172 PDTNGYCLPDQYGSKILFLKENVKNIDKAIISVHCHNDLGLATANSIAGLQNGARQVECT 231 Query: 258 INGIGERAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKA 317 INGIGERAGN S EEVVM L I GL+T I+ + S MV + +QP+KA Sbjct: 232 INGIGERAGNTSMEEVVMILKTHKI---LGLNTQIDATRFYEMSHMVRNQMNMPVQPNKA 288 Query: 318 LVGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEE 377 +VG NAF H SGIHQDG LK+R YEII PED+G + TIVL SGR AL++ L+ Sbjct: 289 IVGGNAFSHSSGIHQDGFLKNRENYEIIKPEDVGFPDA---TIVLTARSGRHALKHHLDR 345 Query: 378 LGYKLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVS 414 LG+KL+ ++ V+ QF +A+ K+ I D DL LV+ Sbjct: 346 LGHKLEKDHLDIVYKQFLVLADSKQGINDQDLNQLVA 382 Lambda K H 0.318 0.134 0.390 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: 527 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 540 Length of database: 386 Length adjustment: 33 Effective length of query: 507 Effective length of database: 353 Effective search space: 178971 Effective search space used: 178971 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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