Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_041246148.1 GURA_RS18920 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000016745.1:WP_041246148.1 Length = 511 Score = 444 bits (1143), Expect = e-129 Identities = 247/514 (48%), Positives = 335/514 (65%), Gaps = 19/514 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 ++I DTTLRDGEQSPGA+M +KL A+QL KL VD+IEAGFP AS+ DF AVK IA+ Sbjct: 6 IKIFDTTLRDGEQSPGASMNIDEKLRLAKQLQKLNVDVIEAGFPIASEGDFEAVKKIAQT 65 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHA-KRPRLRTFIATSPIHMEYKLRKSK 143 + P I G+ R + KDI AWEAL++A +R R+ TFIATS IHM+YKL+ + Sbjct: 66 IKG--------PEIAGLCRSSFKDIDRAWEALQYAGERGRIHTFIATSDIHMKYKLKMTP 117 Query: 144 DQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGI 203 QVLE+A VK AR+ +++F EDA R+D +FL ++ G VI AGAT + IPDTVG Sbjct: 118 KQVLESAVKAVKRARTY-TPNVEFSCEDAVRTDLKFLAEVVGAVIDAGATVVNIPDTVGY 176 Query: 204 AMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGE 263 +PFEY +I +K N +E A+++ HCHNDLGL+ AN+I + GA Q+E TINGIGE Sbjct: 177 TIPFEYFNIIKYLKDNVANVEKAVISVHCHNDLGLSVANSIAAVQAGAGQVECTINGIGE 236 Query: 264 RAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANA 323 RAGN S EE VM L R DIL T + T + S+++ +G+ +QP+KA+VGANA Sbjct: 237 RAGNCSLEEFVMTLKTRQ-DIL-PFKTNVVTEQLTPASRLLTTVTGIVVQPNKAIVGANA 294 Query: 324 FLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLK 383 F HE+GIHQ GM+ + TYEI++PE +GL S +VLGK SGR A + RLEELGY L Sbjct: 295 FAHEAGIHQHGMMMDKTTYEIMTPESVGLKAS---ALVLGKHSGRHAFKKRLEELGYDLD 351 Query: 384 DTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATV 443 D ++ F +FKA+A+ KK + D DL A+V++E + +KL + VTCG+ +TATV Sbjct: 352 DEKLNRAFDRFKALADLKKEVFDEDLDAIVADEVLTAEEKYKLSHITVTCGSFAVATATV 411 Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503 ++ IDG +G GPVD+ KAI + K AKL++Y +G+IT G DA +V ++ Sbjct: 412 QM-EIDGIQVRTAELGDGPVDATLKAIKKLTKTKAKLLQYNVGSITGGTDAQGEVTVRLT 470 Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 G G G TD++ +S AY+ ALN +L Sbjct: 471 DGAR---TVIGRGASTDIIEASAKAYIHALNRLL 501 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: 631 Number of extensions: 22 Number of successful extensions: 8 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: 540 Length of database: 511 Length adjustment: 35 Effective length of query: 505 Effective length of database: 476 Effective search space: 240380 Effective search space used: 240380 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: 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