Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate 14220 b0074 2-isopropylmalate synthase (NCBI)
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Keio:14220 Length = 523 Score = 363 bits (933), Expect = e-105 Identities = 218/515 (42%), Positives = 314/515 (60%), Gaps = 19/515 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQ+ A+++ +KL+ A L ++GVD++E GFP +S DF +V+ IA + Sbjct: 5 VIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQTIARQ 64 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 V N + ++RC EKDI A E+LK A+ R+ TFIATSP+H+ KLR + D Sbjct: 65 VKNSR--------VCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSTLD 116 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 +V+E A MVK AR+ D++F EDA R+ L ++ I AGATT+ IPDTVG Sbjct: 117 EVIERAIYMVKRARNY-TDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYT 175 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 MPFE+ +I+ + P I+ AI++ H H+DLGLA N++ GARQ+E +NGIGER Sbjct: 176 MPFEFAGIISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQVEGAMNGIGER 235 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGN S EEV+MA+ R DIL +HT IN + I +TS++V + + + +KA+VG+ AF Sbjct: 236 AGNCSLEEVIMAIKVRK-DIL-NVHTAINHQEIWRTSQLVSQICNMPIPANKAIVGSGAF 293 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 H SGIHQDG+LK+R YEI++PE IGL + + L SGR A+++R++E+GYK + Sbjct: 294 AHSSGIHQDGVLKNRENYEIMTPESIGLNQI---QLNLTSRSGRAAVKHRMDEMGYKESE 350 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQP-IWKLGDLQVTCGTVGFSTATV 443 ++ ++ F +A+KK ++ D DL AL E+P ++L V G+ +TA V Sbjct: 351 YNLDNLYDAFLKLADKKGQVFDYDLEALAFIGKQQEEPEHFRLDYFSVQSGSNDIATAAV 410 Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503 KL + + + G GPVD+ Y+AIN I + +LVKY+L A G DA + Sbjct: 411 KL-ACGEEVKAEAANGNGPVDAVYQAINRITEYNVELVKYSLTAKGHGKDALGQVDIV-- 467 Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNMLR 538 + N F G G TD+V SS A + LNN+ R Sbjct: 468 -ANYNGRRFHGVGLATDIVESSAKAMVHVLNNIWR 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: 611 Number of extensions: 26 Number of successful extensions: 6 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: 523 Length adjustment: 35 Effective length of query: 505 Effective length of database: 488 Effective search space: 246440 Effective search space used: 246440 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