Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate 3607175 Dshi_0596 2-isopropylmalate synthase (RefSeq)
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Dino:3607175 Length = 525 Score = 415 bits (1066), Expect = e-120 Identities = 244/514 (47%), Positives = 329/514 (64%), Gaps = 20/514 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQSPGA MT +KLE A L ++GVDIIEAGFP AS DF AV IA+ Sbjct: 10 VLIFDTTLRDGEQSPGATMTHDEKLEIAALLDEMGVDIIEAGFPIASDGDFAAVSEIAK- 68 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 N VI G++R N KDI WEA++HA++PR+ TFI TSP+H + D Sbjct: 69 -------NSVNSVICGLARANFKDIDRCWEAVRHARQPRIHTFIGTSPLHRAIP-NLTMD 120 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 ++ + + V AR+L C ++Q+ DA R++ ++L ++ IKAGATT+ IPDTVG Sbjct: 121 EMADRIHDTVTHARNL-CDNVQWSPMDATRTEYDYLCRVIEIAIKAGATTINIPDTVGYT 179 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P E LIA + A+ PG E+ ATHCHNDLG+ATAN + GARQ+E TING+GER Sbjct: 180 APRESADLIARLIADVPGAEDVTFATHCHNDLGMATANALAAVDAGARQVECTINGLGER 239 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGN + EEVVMAL R DI+ T I+TR I+ S+ V SG +Q +KA+VG NAF Sbjct: 240 AGNTALEEVVMALRVRN-DIM-PYQTRIDTRKIMNISRRVAAVSGFAVQFNKAIVGKNAF 297 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDGMLK+ T+EI+ PEDIGL + +V+GK SGR ALR +L++LGY+L D Sbjct: 298 AHESGIHQDGMLKNAETFEIMRPEDIGLSET---NLVMGKHSGRAALRAKLKDLGYELAD 354 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFN-EQPIWKLGDLQVTCGTVGFSTATV 443 +++ VF +FKA+A++KK I D DL AL+S + + + + L+V CGT +A + Sbjct: 355 NQLKDVFVRFKALADRKKEIYDEDLVALMSESSSDPARERLSVKFLRVICGTEAPQSADL 414 Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503 L SIDG + G GPVD+ + A+ + A+L Y + A+TEG DA AT +V Sbjct: 415 TL-SIDGVDKQVTAQGDGPVDATFNAVKALFPHTARLQLYQVHAVTEGTDAQATVTV--- 470 Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 R + + + SG TD VV+S AY++ALN ++ Sbjct: 471 RMEEDGRIVSGQAADTDTVVASAKAYVAALNRLI 504 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: 602 Number of extensions: 26 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: 525 Length adjustment: 35 Effective length of query: 505 Effective length of database: 490 Effective search space: 247450 Effective search space used: 247450 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