Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate 208494 DVU2981 2-isopropylmalate synthase (TIGR)
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__DvH:208494 Length = 509 Score = 442 bits (1138), Expect = e-128 Identities = 241/514 (46%), Positives = 324/514 (63%), Gaps = 17/514 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 +RI DTTLRDGEQSPGA M +KL A QL LGVDIIEAGFP AS DF +V+ IA+ Sbjct: 5 IRIFDTTLRDGEQSPGATMNIKEKLRLAHQLQTLGVDIIEAGFPAASPGDFESVRAIAKT 64 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 V + G+ R DI AW+A+ A+ PRL TF+ATSP+HM+YKLRK+ D Sbjct: 65 VKGMT--------VAGLCRALPADIDRAWDAVCVAESPRLHTFLATSPVHMQYKLRKTPD 116 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 +V+ V+ A ++++F AEDA+RSD++FL ++F I+AGATT+ IPDTVG A Sbjct: 117 EVVRMVDAAVRHAAG-HTSNVEFSAEDASRSDRDFLVRVFTTAIEAGATTINIPDTVGYA 175 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P E+G L+ + NTP A+ + HCHNDLGL ANT+ R GARQ EVTI+GIGER Sbjct: 176 QPEEFGALVRYVIENTPNAHKAVFSVHCHNDLGLGVANTLAALRAGARQAEVTISGIGER 235 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGNA+ EE+VMAL R GL TGI T + T +++ G + +KA+VGANAF Sbjct: 236 AGNAALEELVMALRTR--HDYFGLDTGIVTEQLYPTCRLLSMIIGQPIPANKAIVGANAF 293 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDGMLKHR TYEI++PE IG R+ +VLGK SGR A++N+LEELGY+L++ Sbjct: 294 AHESGIHQDGMLKHRETYEIMTPESIGRTRT---ELVLGKHSGRNAVKNKLEELGYRLEE 350 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVK 444 ++ VF K +A+KKK+I D D+ ALV E + ++L +L V C G Sbjct: 351 DQLNTVFDAVKQLADKKKQIHDEDVEALVLEEVYRIPDRYRLVNLSVQCSDTGMPPTAAV 410 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 + +DG G GP+D+ + AI HIV +L +Y++ AIT G DA +V + Sbjct: 411 VMEVDGETMRHAGFGAGPIDAVFNAIAHIVGRTPQLERYSVTAITGGTDAQGEVTVRVRE 470 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNMLR 538 N G G D++++S AYL+ALN +++ Sbjct: 471 ---NGGTAVGRGSHPDIIIASARAYLNALNRLVK 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: 662 Number of extensions: 30 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: 509 Length adjustment: 35 Effective length of query: 505 Effective length of database: 474 Effective search space: 239370 Effective search space used: 239370 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 Jul 25 2024. The underlying query database was built on Jul 25 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