Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate Dsui_3519 Dsui_3519 2-isopropylmalate synthase, bacterial type
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__PS:Dsui_3519 Length = 513 Score = 431 bits (1108), Expect = e-125 Identities = 247/512 (48%), Positives = 328/512 (64%), Gaps = 20/512 (3%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTTLRDGEQSPGA+MT +KL ARQL ++ VD+IEAGF AS DF A+ IAE + Sbjct: 7 IFDTTLRDGEQSPGASMTKEEKLRVARQLERMRVDVIEAGFAAASPGDFDAIHAIAEAIK 66 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + + ++R NE DI A EA+K A R R+ TFIATSPIHME KLR S DQV Sbjct: 67 DST--------VCSLARANENDIRRAGEAIKPAARGRIHTFIATSPIHMEKKLRMSPDQV 118 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 +E A + +AR D++F AEDA RS+ +FL +IF VIKAGATT+ +PDTVG +P Sbjct: 119 VEQAVKAIGWAREY-TNDVEFSAEDAGRSEIDFLCRIFEAVIKAGATTINVPDTVGYNLP 177 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGERAG 266 ++ + I + PG + + + HCHNDLGLA AN++ GARQ+E TING+GERAG Sbjct: 178 SQFAETIRQLIERVPGADKVVWSVHCHNDLGLAVANSLAAVLAGARQVECTINGLGERAG 237 Query: 267 NASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFLH 326 NAS EEVVMA R DI + T ++T I+ SK+V + +G +QP+KA+VGANAF H Sbjct: 238 NASLEEVVMATRTRA-DIF-PVETRVDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAH 295 Query: 327 ESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKDTE 386 ESGIHQDG+LKHR TYEI+ ED+G + + +VLGK SGR A + RL ELG L E Sbjct: 296 ESGIHQDGVLKHRETYEIMRAEDVGWSQ---NKLVLGKHSGRNAFKTRLAELGIDLPSEE 352 Query: 387 -VEGVFWQFKAVAEKKKRITDTDLRALVSNEAFN-EQPIWKLGDLQVTCGTVGFSTATVK 444 + F +FK +A+KK I D DL+ALVS+E EQ +KL QV C G + Sbjct: 353 ALNAAFARFKELADKKHEIFDEDLQALVSDETVTPEQEHYKLVYSQV-CSETGEIPESAV 411 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 ++ G+ H A S G+GPVD+ +KAI I A+ + Y++ AIT G DA +V +++ Sbjct: 412 TLAVGGAEHKAASSGSGPVDATFKAIEKIAASGAEQLLYSVNAITTGTDAQGEVTVRLAK 471 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 G + +G G TD+V++S AYL+ALN + Sbjct: 472 GGR---IVNGQGADTDIVIASAKAYLNALNKL 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: 630 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: 513 Length adjustment: 35 Effective length of query: 505 Effective length of database: 478 Effective search space: 241390 Effective search space used: 241390 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