Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate N515DRAFT_0574 N515DRAFT_0574 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Dyella79:N515DRAFT_0574 Length = 535 Score = 389 bits (1000), Expect = e-112 Identities = 221/515 (42%), Positives = 320/515 (62%), Gaps = 19/515 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 VRI DTTLRDGEQ+PG M KL A L LGVD++EAGFP AS DF AV IA+ Sbjct: 22 VRIFDTTLRDGEQAPGFGMDRRAKLRMAHALEALGVDVMEAGFPQASPDDFAAVADIAKA 81 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 V + + ++RC DI TA AL+ A+ R+ F++TSP+H E+KL SK Sbjct: 82 VRHST--------VCALARCQAADIDTAGRALEAAQHSRIHVFLSTSPLHREHKLGMSKQ 133 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 QV++TA V+ AR+L C +++F AEDA R++ ++L ++F I AGATT+ PDTVG Sbjct: 134 QVIDTAIAAVERARAL-CHEVEFSAEDAMRTEPDYLAEVFSAAIAAGATTVNAPDTVGYV 192 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P E + A ++ + G E + ++HCH+DLG+A AN++ GARQ+E TINGIGER Sbjct: 193 TPAEIAERFAYLRKHVKGAERVVFSSHCHDDLGMAVANSLAAVSAGARQIECTINGIGER 252 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGNAS EEVVMAL RG G+ + I+ R +++TS+++ + +G + +KA+VG NAF Sbjct: 253 AGNASLEEVVMALRVRGPYF--GVDSRIDARRLVQTSRLLTQLTGQAVPRNKAIVGDNAF 310 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDT-IVLGKLSGRQALRNRLEELGYKLK 383 HESGIHQ GMLKHRGTYEI+ P+D+G+ G+T +VLGK SGR ALR+RL+ LG+ + Sbjct: 311 AHESGIHQHGMLKHRGTYEIMRPQDVGM----GETKLVLGKHSGRHALRSRLQALGHTPE 366 Query: 384 DTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATV 443 + ++ +F +FKA+A+KK+ I D DL AL + + W++ L + G ++A+V Sbjct: 367 EAAMDDIFARFKALADKKREIHDEDLEALALGQDPDAAGPWRIVQLNSSSHLGGSASASV 426 Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503 +L DG +IG GPVD+ +A+ +L ++ + A++EG DA + Sbjct: 427 RLAHDDGREIGEAAIGDGPVDAVLRAMERATGTDLELTQFQVRAVSEGGDAQGQAQLTAR 486 Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNMLR 538 N + G G TD+V ++ A LS +N + R Sbjct: 487 HAARN---WRGNGVSTDIVEATALAALSIVNRIER 518 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: 607 Number of extensions: 26 Number of successful extensions: 5 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: 535 Length adjustment: 35 Effective length of query: 505 Effective length of database: 500 Effective search space: 252500 Effective search space used: 252500 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 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