Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012410426.1 NPUN_RS20595 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000020025.1:WP_012410426.1 Length = 540 Score = 452 bits (1164), Expect = e-131 Identities = 252/529 (47%), Positives = 346/529 (65%), Gaps = 24/529 (4%) Query: 22 PTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMI 81 P V I DTTLRDGEQSPGA + +KL A QLA LGVD+IEAGF AS DF AVK I Sbjct: 7 PDRVIIFDTTLRDGEQSPGATLNVEEKLAIAHQLALLGVDVIEAGFAVASPGDFQAVKTI 66 Query: 82 AEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRK 141 AE+VG + G P+I ++R +DI A EALK A RPR+ T I+TS IH++Y+L+K Sbjct: 67 AEQVG--IPGG---PIICSLARAIRQDIHAAAEALKGAARPRIHTMISTSDIHLKYQLKK 121 Query: 142 SKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTV 201 S+ +VL A MV +A+S D++F DA+R++ EFLY++ I AGATT+ IPDTV Sbjct: 122 SRSEVLAIASEMVAYAKSF-VDDVEFSPMDASRTEPEFLYEVLEAAIAAGATTINIPDTV 180 Query: 202 GIAMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGI 261 G P E G LI I+ + P I+ I++ H NDLGLATAN + YG RQ+E TINGI Sbjct: 181 GYCTPKEIGTLIQGIREHVPNIDGVILSIHTQNDLGLATANALAAIEYGVRQVECTINGI 240 Query: 262 GERAGNASFEEVVMALTC----------RGIDILGGLHTGINTRHILKTSKMVEKYSGLH 311 GERAGNA+ EE+VMAL R +D L T I T+ I KTS +V + +G+ Sbjct: 241 GERAGNAALEEIVMALQVRKPFFNPYFGRPVDADTPL-TNIKTQEIYKTSSLVSQLTGML 299 Query: 312 LQPHKALVGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQAL 371 +QP+KA+VGANAF HESGIHQDG++KHR TYEI+ IGL + IVLGK SGR A Sbjct: 300 IQPNKAIVGANAFAHESGIHQDGIIKHRQTYEIMEAAAIGLPE---NRIVLGKHSGRNAF 356 Query: 372 RNRLEELGYKLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEA-FNEQPIWKLGDLQ 430 R RL+ELG++L + ++ F +FK VA+KKK I+D DL A+V +E + +++ +Q Sbjct: 357 RTRLKELGFELNEADLNKAFNRFKDVADKKKEISDWDLEAIVRDETQIQVESGFQIEHVQ 416 Query: 431 VTCGTVGFSTATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITE 490 V CG TAT+ + + DG + S+GTGPVD+ Y+AIN +V+ P +L+++++ ++T Sbjct: 417 VICGDCTCPTATITIVTPDGKILTDASVGTGPVDAVYQAINRLVQIPNQLIEFSVQSVTG 476 Query: 491 GIDATATTSVEISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNMLRF 539 GIDA T +V + + +FSG TD+VV++ A+++ALN + R+ Sbjct: 477 GIDALGTVTVRLKHQER---IFSGQASDTDIVVAAAYAHINALNRLYRY 522 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: 667 Number of extensions: 29 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: 540 Length adjustment: 35 Effective length of query: 505 Effective length of database: 505 Effective search space: 255025 Effective search space used: 255025 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