Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate Echvi_3833 Echvi_3833 Isopropylmalate/homocitrate/citramalate synthases
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Cola:Echvi_3833 Length = 390 Score = 355 bits (911), Expect = e-102 Identities = 195/389 (50%), Positives = 255/389 (65%), Gaps = 15/389 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQ PG + QK+E ARQL LGVD+IEAGFP +S DF +V I++ Sbjct: 6 VLIFDTTLRDGEQVPGCKLNTPQKIEIARQLESLGVDVIEAGFPISSPGDFKSVVEISKS 65 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 V P+I G+SR KDI A EALK+AKRPR+ T I TSP H++YK + + D Sbjct: 66 VSE--------PIICGLSRGVAKDIEVAAEALKYAKRPRIHTGIGTSPSHIKYKFKSTPD 117 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 Q+LE A VK A+S D++F AEDA R+D E+L +I V+KAGAT L IPDT G Sbjct: 118 QILERAVAAVKHAKSF-VEDVEFYAEDAGRTDNEYLARICEAVVKAGATVLNIPDTTGYC 176 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 +P EYG I + N GIEN I++ HCHNDLGLATAN+I GARQ+E TINGIGER Sbjct: 177 LPDEYGAKIKYLMDNVKGIENVIISAHCHNDLGLATANSISAVMNGARQIECTINGIGER 236 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGN S EEV M + ++ IN+R + S++V + G+H+QP+KA+VG+NAF Sbjct: 237 AGNTSLEEVAMIMKQHP---RLNVYNKINSRLLNPISRLVSERMGMHVQPNKAIVGSNAF 293 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 H SGIHQDG++K+R TYEII PE++G+ S+ IVL SGR AL RL ++GY + Sbjct: 294 AHSSGIHQDGVIKNRETYEIIDPEEVGVTESM---IVLTARSGRAALAFRLHKIGYTITK 350 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALV 413 +++ ++ F A+ KK ITD DL ++ Sbjct: 351 LQLDDIYQLFLEHADMKKEITDEDLHEIM 379 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: 502 Number of extensions: 21 Number of successful extensions: 5 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: 390 Length adjustment: 33 Effective length of query: 507 Effective length of database: 357 Effective search space: 180999 Effective search space used: 180999 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: 51 (24.3 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