Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate GFF1023 Psest_1056 2-isopropylmalate synthase, bacterial type
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__psRCH2:GFF1023 Length = 514 Score = 434 bits (1116), Expect = e-126 Identities = 246/513 (47%), Positives = 329/513 (64%), Gaps = 19/513 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQSPGA+MT +KL AR L +L VD+IEAGF AS DF AVK++A+ Sbjct: 7 VIIFDTTLRDGEQSPGASMTAEEKLRIARALERLKVDVIEAGFAIASPGDFAAVKLVADN 66 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 + + + ++R + DI A EAL A R+ TFIATSPIHM+YKLR D Sbjct: 67 IKDST--------VCSLARAVDADIERAAEALAGANSGRIHTFIATSPIHMQYKLRMQPD 118 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 QV+E A VK ARSL C D++F EDA RS+ +FL +I I AGA T+ IPDTVG A Sbjct: 119 QVVEQAVRAVKKARSL-CADVEFSCEDAGRSEIDFLCRIIKAAIDAGARTINIPDTVGYA 177 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 +P +Y I + P + A+ + HCHNDLGLA AN++ GARQ+E TING+GER Sbjct: 178 IPHQYADTIRQLLERIPNADKAVFSVHCHNDLGLAVANSLAAVVAGARQVECTINGLGER 237 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGNA+ EE+VMA+ R L +HT I T HIL S++V +G +QP+KA+VGANAF Sbjct: 238 AGNAALEEIVMAIKTR--QDLINVHTRIETEHILAASRLVSGITGFPVQPNKAIVGANAF 295 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDG+LKHR TYEI+S + +G + +V+GK SGR A R+RL+ELG L+ Sbjct: 296 AHESGIHQDGVLKHRETYEIMSAQSVGW---NANKMVMGKHSGRAAFRSRLDELGIVLEG 352 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQP-IWKLGDLQVTCGTVGFSTATV 443 E+ F +FK +A+KK I D DL+ALVS+ +E P +KL L+V T A + Sbjct: 353 DELNAAFARFKELADKKHEIFDEDLQALVSDTLADEAPEHFKLASLEVASKTGTIPEAKL 412 Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503 + S+DG+ A + G+GPVD+ +KAI + + A L Y++ AIT+G D+ +V + Sbjct: 413 -VISVDGAERSAQAQGSGPVDATFKAIEAVAESGATLQLYSVNAITQGTDSQGEVTVRLE 471 Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 +G + +G G TD+VV+S AYL+ALN M Sbjct: 472 KGGR---IVNGNGADTDIVVASAKAYLNALNLM 501 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: 630 Number of extensions: 22 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: 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 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