Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_020565658.1 A3OW_RS0122190 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000372865.1:WP_020565658.1 Length = 514 Score = 400 bits (1028), Expect = e-116 Identities = 236/512 (46%), Positives = 321/512 (62%), Gaps = 20/512 (3%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTT+RDGEQSPGA+MT +K+ + L +L VD+IEAGFP AS DF AV+ +A + Sbjct: 7 IFDTTMRDGEQSPGASMTRDEKIRIGKALERLKVDVIEAGFPAASPGDFEAVQAVANVIK 66 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + + G++R +KDI +A ALK A R R+ TFIATSPIHM+ KL +QV Sbjct: 67 DST--------VCGLARALDKDIDSAGLALKGAARSRIHTFIATSPIHMQMKLHMQPEQV 118 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 +E A VK AR D++F EDA RS+++FL +I VI AGATTL IPDTVG ++P Sbjct: 119 IEYAVRAVKRARQY-TDDVEFSPEDAGRSEEDFLCRILEAVIDAGATTLNIPDTVGYSIP 177 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGERAG 266 ++G IA++ P + A+ + HCHNDLGLA AN++ GARQ+E TING+GERAG Sbjct: 178 QQFGATIANLIKRIPNSDKAVFSVHCHNDLGLAVANSLSAVMNGARQIECTINGLGERAG 237 Query: 267 NASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFLH 326 NAS EEVVMA+ R D+ TGI+TR IL SK+V +G +QP+KA+VGANAF H Sbjct: 238 NASLEEVVMAVRTRQ-DVF-TCDTGIDTREILTCSKLVSSITGFPVQPNKAIVGANAFAH 295 Query: 327 ESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKL-KDT 385 E+GIHQDG+LK R TYEI+ ED+G + +VLGK SGR A ++R+ ELG + + Sbjct: 296 EAGIHQDGVLKSRETYEIMRAEDVGW---SANRMVLGKHSGRNAFKSRMTELGIEFTSEE 352 Query: 386 EVEGVFWQFKAVAEKKKRITDTDLRALVSNEAF-NEQPIWKLGDLQVTCGTVGFSTATVK 444 E+ VF +FK +A+KK I D DL+AL+S +F +E KL L+V T A V Sbjct: 353 ELNDVFLRFKQLADKKHDIFDEDLQALISEASFESEDEYVKLISLKVCSETGEVPNAKVT 412 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 L ID S G G VD++ KAI +V A L Y++ IT G D+ +V + + Sbjct: 413 L-RIDNKEVTGNSHGGGAVDASLKAIEQLVMSNASLELYSVNNITNGTDSQGEVTVRLEK 471 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 + +G G TD+V++S AY++A+N + Sbjct: 472 ---EGRIVNGLGADTDIVIASAKAYINAVNKL 500 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: 654 Number of extensions: 25 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: 514 Length adjustment: 35 Effective length of query: 505 Effective length of database: 479 Effective search space: 241895 Effective search space used: 241895 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