Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_092483010.1 BM299_RS08305 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_900115975.1:WP_092483010.1 Length = 508 Score = 444 bits (1141), Expect = e-129 Identities = 252/513 (49%), Positives = 330/513 (64%), Gaps = 16/513 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQSPG ++ +KLE ARQLA+LGVDIIEAGFP S DF AVK IA E Sbjct: 5 VYIFDTTLRDGEQSPGVSLNASEKLEIARQLARLGVDIIEAGFPITSNGDFEAVKTIARE 64 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 V + G++R N DI AWEA+KHA +PR+ TFIATS IHM +KLR ++D Sbjct: 65 VRGVT--------VAGLARTNFADIDRAWEAVKHADQPRIHTFIATSDIHMTHKLRMNRD 116 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 QV+E A VK A+S +D++F AEDA+RSD +FL ++ I AGATT+ IPDTVG A Sbjct: 117 QVVEAAVAGVKHAKSY-TSDVEFSAEDASRSDLDFLCRVVEAAIGAGATTINIPDTVGYA 175 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P E+ I I GIE +++ HCH+DLGLA +N++ GARQ+E INGIGER Sbjct: 176 TPDEFAAFIRSIMNRVSGIEKVVLSVHCHDDLGLAVSNSLAAVLAGARQVEGAINGIGER 235 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGNAS EEVVMAL R GL TGI T I +TSK+V K +G+ +QP+KA+VG NAF Sbjct: 236 AGNASIEEVVMALYTRRDRY--GLETGIRTEEIYRTSKLVSKLTGMDIQPNKAVVGKNAF 293 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDG+LK R TYEI++P +G+ S +VLGK SGR A R+RL ELG+ L + Sbjct: 294 AHESGIHQDGVLKERTTYEIMNPAMVGISHS---NLVLGKHSGRHAFRSRLVELGFVLSE 350 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVK 444 E+ F +FK +A++KK ITD DL A+V NE + L L + GT TATV Sbjct: 351 DELNKAFARFKDLADRKKEITDHDLEAIVENEIRKVPATYDLSYLHTSSGTTVVPTATVG 410 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 L + + A + G GPVD+ KA++ I +L + + AIT G DA ++ I+ Sbjct: 411 LLRGEELLEEA-ACGNGPVDAICKAVDKITGYSCRLASWGINAITAGKDALGEVTLRIAE 469 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 + + ++ G G TDV+ +S AY++A+N M+ Sbjct: 470 NNKD-KLYMGRGISTDVLEASARAYVNAVNKMI 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: 616 Number of extensions: 30 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: 508 Length adjustment: 35 Effective length of query: 505 Effective length of database: 473 Effective search space: 238865 Effective search space used: 238865 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