Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_011813495.1 HHAL_RS03550 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000015585.1:WP_011813495.1 Length = 516 Score = 405 bits (1040), Expect = e-117 Identities = 234/516 (45%), Positives = 325/516 (62%), Gaps = 20/516 (3%) Query: 24 YVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAE 83 ++ I DTTLRDGEQSPGA+MT +K+ A+ L ++ VD++EAGFP AS DF +V+ +AE Sbjct: 6 HLYIFDTTLRDGEQSPGASMTREEKVRIAKGLERMRVDVLEAGFPAASTGDFESVRAVAE 65 Query: 84 EVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSK 143 + + ++R + DI A EAL A+ R+ TFIATSPIHM+ KL + Sbjct: 66 AIKESR--------VCALARARDPDIHAAGEALAQAEAGRIHTFIATSPIHMQNKLHMTP 117 Query: 144 DQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGI 203 DQV++ A + V AR L C D++F EDA RS+ +FL +I I AGA T+ IPDTVG Sbjct: 118 DQVVDAAVHAVSLARQL-CDDVEFSPEDAGRSEHDFLCRIIEAAIDAGARTINIPDTVGY 176 Query: 204 AMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGE 263 +P ++G LI ++ P + A+ + HCHNDLG+A AN++ + GARQ+E TING+GE Sbjct: 177 NLPEQFGGLIRTLRERIPNSDKAVFSVHCHNDLGVAVANSLAAVQAGARQVECTINGLGE 236 Query: 264 RAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANA 323 RAGNA+ EEVVMA+ R D+ T IN R I+ TSK+V +G H+QP+KA+VG NA Sbjct: 237 RAGNAALEEVVMAVKTRQ-DVF-SCSTRINAREIVPTSKLVANITGFHVQPNKAIVGVNA 294 Query: 324 FLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKL- 382 F HESGIHQDG+LKHR TYEI+ ED+G + +VLGK SGR A R+RLEEL L Sbjct: 295 FAHESGIHQDGVLKHRETYEIMRAEDVGWHT---NRMVLGKHSGRNAFRSRLEELDIHLD 351 Query: 383 KDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNE-AFNEQPIWKLGDLQVTCGTVGFSTA 441 + ++ F +FK +A+KK I D DL+ALV+ A E +L L V T A Sbjct: 352 SEEQLNEAFARFKTLADKKHEIFDEDLQALVTEAGAALENERIRLLALHVCSETGEQPEA 411 Query: 442 TVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVE 501 TV L IDG A + G+G VD+A+ A++ +V+ +L+ Y++ IT G D+ +V Sbjct: 412 TVSLL-IDGEERQAVAPGSGAVDAAFMAVDSLVQSGTELLLYSVNNITSGTDSQGEVTVR 470 Query: 502 ISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 + RG V +G G D+V++S AY++ALN +L Sbjct: 471 LERGGR---VANGQGADVDIVIASAKAYINALNKIL 503 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: 640 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: 516 Length adjustment: 35 Effective length of query: 505 Effective length of database: 481 Effective search space: 242905 Effective search space used: 242905 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