Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012113349.1 XAUT_RS06660 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000017645.1:WP_012113349.1 Length = 527 Score = 399 bits (1025), Expect = e-115 Identities = 227/512 (44%), Positives = 315/512 (61%), Gaps = 18/512 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQ PGA+MT +KLE A L ++GVD+IEAGFP AS DF +V IA Sbjct: 20 VVIFDTTLRDGEQCPGASMTFEEKLEVAALLDEMGVDVIEAGFPIASIGDFESVAEIARR 79 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 N + G+SR DI EA+KHA+R R+ TF++TSP+HM+YKL+K Sbjct: 80 TQNAT--------VAGLSRAALNDIDRCAEAVKHARRGRIHTFLSTSPVHMKYKLQKQPH 131 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 +VLE V AR+ D+++ +ED R++ +FL + IKAGATT+ IPDTVG Sbjct: 132 EVLEMVVASVTRARN-HVEDVEWSSEDGTRTEIDFLCRCVEAAIKAGATTINIPDTVGYT 190 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P EY L + P + AI + HCH+DLG+A AN++ G GARQ+E T+NGIGER Sbjct: 191 TPAEYEALFRTVIERVPNSDKAIFSVHCHDDLGMAVANSLAGLAGGARQIECTVNGIGER 250 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGNA+ EEVVMA+ R D+L +GINT+ + + SK+V + +Q +KA+VG NAF Sbjct: 251 AGNAALEEVVMAIETRS-DVL-PYRSGINTKMLTRASKLVSAVTSFPVQYNKAIVGRNAF 308 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDGMLKH TYEI++PE +G+ ++ ++V+GK SGR A R++L+ +GY+L + Sbjct: 309 AHESGIHQDGMLKHTQTYEIMTPESVGVSKT---SLVMGKHSGRAAFRDKLKTMGYELGE 365 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVK 444 + F +FK +A++KK + D D+ ALV KL L V GT G AT++ Sbjct: 366 NALNDAFTRFKDLADRKKVVYDEDIEALVDQGIAAAYDRIKLISLSVIAGTRGPQRATMR 425 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 L +DG + + G GPVD+ + AI +V KL Y + A+TEG DA A SV + Sbjct: 426 L-EVDGQVKTEEAEGNGPVDATFNAIKALVPHQVKLDLYQVHAVTEGTDAQAEVSVRL-- 482 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 + N + D +V+S AY++ALN + Sbjct: 483 -EENGKAVTARAADPDTLVASAQAYITALNKL 513 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: 651 Number of extensions: 28 Number of successful extensions: 7 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: 527 Length adjustment: 35 Effective length of query: 505 Effective length of database: 492 Effective search space: 248460 Effective search space used: 248460 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