Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate GFF2606 PGA1_c26470 2-isopropylmalate synthase LeuA
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Phaeo:GFF2606 Length = 523 Score = 410 bits (1053), Expect = e-119 Identities = 238/513 (46%), Positives = 327/513 (63%), Gaps = 20/513 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQSPGA MT +KLE A L +GVDIIEAGFP AS+ DF AV IAE Sbjct: 10 VLIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFKAVSEIAER 69 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 N I G++R N KDI EA+K A +PR+ TFI TSP+H +KD Sbjct: 70 SKNSR--------ICGLARANFKDIDRCAEAVKRAAQPRIHTFIGTSPLHRAIP-NLTKD 120 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 ++ E + V AR+L ++Q+ DA R++ ++L ++ IKAGATT+ IPDTVG Sbjct: 121 EMAEKIHDTVTHARNL-VDNVQWSPMDATRTEWDYLCRVIEIAIKAGATTINIPDTVGYT 179 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P E LI + PG ++ I ATHCHNDLG+ATAN++ GARQ+E TING+GER Sbjct: 180 APVESADLIKRLIETVPGADDVIFATHCHNDLGMATANSLAAVAGGARQIECTINGLGER 239 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGN + EEVVMAL R DI+ TGI+T+ I+ S+ V SG +QP+KA+VG NAF Sbjct: 240 AGNTALEEVVMALKVRN-DIM-PFTTGIDTQKIMHISRRVSTVSGFVVQPNKAIVGKNAF 297 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDGMLK++ T+EI+ PED+G+ G ++ LGK SGR ALR++L +LG+++ D Sbjct: 298 AHESGIHQDGMLKNKETFEIMRPEDVGI---AGTSLPLGKHSGRAALRDKLSQLGFEVGD 354 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVK 444 +++ +F +FK +A++KK + D D+ AL+ +E KL ++V CGT G + AT++ Sbjct: 355 NQLKDLFVRFKELADRKKEVFDDDIIALMRTSG-DEDDHLKLVSMKVVCGTGGPAEATLE 413 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 + ++G + G GPVD+A++AI I A L Y + A+TEG DA AT SV + Sbjct: 414 M-EVEGKDVSETAEGDGPVDAAFRAIRKIHPNSAHLQLYQVHAVTEGTDAQATVSVRL-- 470 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 + N + +G TD VV+S AY+ ALN ++ Sbjct: 471 -EENGVIATGESANTDTVVASAAAYIGALNRLI 502 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: 641 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: 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