Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate GFF555 HP15_538 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Marino:GFF555 Length = 516 Score = 410 bits (1053), Expect = e-119 Identities = 235/518 (45%), Positives = 325/518 (62%), Gaps = 20/518 (3%) Query: 19 IPNPTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAV 78 +P ++ I DTTLRDGEQSPGA M +KL A+ L KL VD+IEAGF AS+ DF AV Sbjct: 1 MPATDHLVIFDTTLRDGEQSPGATMNKAEKLRIAKALEKLRVDVIEAGFAIASQGDFEAV 60 Query: 79 KMIAEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYK 138 K IAE + + I ++R +KDI A EA++ A+R R+ TFIATSPIHM++K Sbjct: 61 KAIAESIKDST--------ICSLARALDKDIDRAAEAIRPAQRGRIHTFIATSPIHMKHK 112 Query: 139 LRKSKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIP 198 L+ D+V+E A VK ARS D++F EDA RS+ +FL +I I AGA+T+ IP Sbjct: 113 LQMQPDEVIEQAVRSVKRARS-HVDDVEFSCEDAGRSELDFLCRIIEAAIDAGASTINIP 171 Query: 199 DTVGIAMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTI 258 DTVG A+P ++G+ I + P + AI + HCHNDLGLA +N++ GARQ+E TI Sbjct: 172 DTVGYAIPEQFGETIRQLLNRIPNADKAIFSVHCHNDLGLAVSNSLAAVSQGARQVECTI 231 Query: 259 NGIGERAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKAL 318 NG+GERAGNA+ EE+VMA+ R L + T I+ +HI+ S++V +G +QP+KA+ Sbjct: 232 NGLGERAGNAALEEIVMAVRTR--QDLFHIDTRIDAQHIVPASRLVSTITGFPVQPNKAI 289 Query: 319 VGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEEL 378 VGANAF HESGIHQDG+LKHR TYEI+ +D+G +++VLGK SGR A R RL EL Sbjct: 290 VGANAFAHESGIHQDGVLKHRETYEIMRAQDVGWHT---NSLVLGKHSGRNAFRTRLLEL 346 Query: 379 GYKLK-DTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQP-IWKLGDLQVTCGTV 436 G + + +TE+ F +FKA+A+ K I D DL+A+ S+ E+ + L +QV C Sbjct: 347 GIQFETETELNEAFTRFKALADLKHEIFDEDLQAIASDTRQKEEDGRYGLVCMQV-CSET 405 Query: 437 GFSTATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATA 496 G S+DG H + G+GPVD+ +KAI +V L Y++ IT G DA Sbjct: 406 GVVPKANLTLSVDGKEHKVEAEGSGPVDATFKAIESLVDSGCNLQLYSVNNITSGTDAQG 465 Query: 497 TTSVEISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALN 534 +V + RG + +G G TD++++S AY+ ALN Sbjct: 466 EVTVRLERGGR---IVNGVGADTDIIIASAKAYIEALN 500 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: 649 Number of extensions: 27 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 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