Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate Synpcc7942_1410 Synpcc7942_1410 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__SynE:Synpcc7942_1410 Length = 540 Score = 454 bits (1168), Expect = e-132 Identities = 258/522 (49%), Positives = 339/522 (64%), Gaps = 23/522 (4%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 + I DTTLRDGEQSPGA++ +KL ARQLA+L VDIIEAGF AS DF AV+ IA E Sbjct: 10 ILIFDTTLRDGEQSPGASLNLEEKLAIARQLARLNVDIIEAGFAFASPGDFEAVQRIAAE 69 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 VG DG P I ++R +DI A EAL A + R+ TFIATS IH+EYKL+K++ Sbjct: 70 VGT-PDG----PTICSLARATRQDIKAAAEALAPAAKGRIHTFIATSDIHLEYKLKKTRA 124 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 +VL MV +A SL D++F EDA RSD EFLY+ I AGA T+ IPDTVG Sbjct: 125 EVLAVIPEMVGYAASL-VDDVEFSPEDAGRSDPEFLYECLEAAIAAGAKTINIPDTVGYT 183 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P E+G LI IK N I+ AI++ H HNDLGLA AN +E + GARQLE TINGIGER Sbjct: 184 TPSEFGALIGGIKQNVCNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGIGER 243 Query: 265 AGNASFEEVVMALTC----------RGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQP 314 AGNA+ EE+VMAL R D L T +NTR I KTS++V +G+ +QP Sbjct: 244 AGNAALEELVMALHVRRQYFNPFLGRAADSEAPL-TQVNTREIYKTSRLVSNLTGMLVQP 302 Query: 315 HKALVGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNR 374 +KA+VGANAF HESGIHQDG+LK++ TYEI+ E IGL + I LGKLSGR A R R Sbjct: 303 NKAIVGANAFAHESGIHQDGVLKNKLTYEIVDAETIGLST---NRITLGKLSGRNAFRTR 359 Query: 375 LEELGYKLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCG 434 L+ELGY L + ++ F +FK +A+KK+ +TD DL A+V++E ++KL +QV+ G Sbjct: 360 LQELGYDLGEDDLNRAFLRFKELADKKREVTDRDLEAIVNDETQQAPELFKLELVQVSAG 419 Query: 435 TVGFSTATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDA 494 TATV L + +G +IGTGPVD+ Y+AIN +V P +L+++++ ++T GIDA Sbjct: 420 DHARPTATVTLRTPEGEELTDAAIGTGPVDAIYRAINRVVNIPNELIEFSVKSVTAGIDA 479 Query: 495 TATTSVEISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 ++ + D +FSG TD++V+S AY+ ALN + Sbjct: 480 IGEVTIRLRHEDR---IFSGHSANTDILVASAQAYIHALNRL 518 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: 612 Number of extensions: 19 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: 540 Length adjustment: 35 Effective length of query: 505 Effective length of database: 505 Effective search space: 255025 Effective search space used: 255025 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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