Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_029135047.1 A3GO_RS0120870 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000428045.1:WP_029135047.1 Length = 514 Score = 409 bits (1051), Expect = e-118 Identities = 243/518 (46%), Positives = 327/518 (63%), Gaps = 20/518 (3%) Query: 21 NPTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKM 80 NP + I DTTLRDGEQSPGA+MT +KL A+ L K+ VDIIEAGFP AS DF AV+ Sbjct: 3 NPDKLFIFDTTLRDGEQSPGASMTKDEKLRIAKALEKMRVDIIEAGFPIASPGDFDAVQT 62 Query: 81 IAEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLR 140 IA + + + G++R E DI A EALK A R+ TFIATSPIHM+ KLR Sbjct: 63 IARTIKDST--------VCGLARALEADIDRAGEALKEANSGRIHTFIATSPIHMQQKLR 114 Query: 141 KSKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDT 200 + DQV+E A VK AR +++F EDA RS+ +FL ++ + I AGATT+ +PDT Sbjct: 115 MTPDQVVEQAVWAVKRARRY-TDNVEFSPEDAGRSEIDFLCRVIEQAIAAGATTINVPDT 173 Query: 201 VGIAMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTING 260 VG +P ++G+ I + P + AI + HCHNDLGLA AN++ GARQ+E TING Sbjct: 174 VGYNLPQQFGETIRTLIERIPNSDKAIFSVHCHNDLGLAVANSLAAVTQGARQVECTING 233 Query: 261 IGERAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVG 320 +GERAGNAS EEVVMA+ R L + ++T I+ S++V +G +QP+KA+VG Sbjct: 234 LGERAGNASLEEVVMAVRTR--RDLFTCDSTLDTTQIVNCSRLVSGITGFPVQPNKAIVG 291 Query: 321 ANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGY 380 ANAF HESGIHQDG+LKHR TYEI+ ED+G + + +V+GK SGR A R RLEELG Sbjct: 292 ANAFAHESGIHQDGVLKHRETYEIMRAEDVGWSQ---NRMVMGKHSGRNAFRTRLEELGI 348 Query: 381 KL-KDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFN-EQPIWKLGDLQVTCGTVGF 438 + E+ F +FK +A+KK I D DL+ALVS+ F+ E KL L+V T Sbjct: 349 TFDSEEEINDAFRRFKDLADKKHEIFDEDLQALVSDAGFSAENEHIKLISLKVCSETGEI 408 Query: 439 STATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATT 498 A V L S+D + G+GPVD+A+KAI +V+ A+L Y++ AIT G DA Sbjct: 409 PNARVVL-SVDEREMSGEASGSGPVDAAFKAIESMVQSNAELQLYSVNAITSGTDAQGEV 467 Query: 499 SVEISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 +V + R N + +G G TD+V++S AY++A+N + Sbjct: 468 TVRLQR---NGGIVNGQGADTDIVIASAKAYVNAVNRL 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: 612 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: 514 Length adjustment: 35 Effective length of query: 505 Effective length of database: 479 Effective search space: 241895 Effective search space used: 241895 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