Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate 5211056 Shew_3472 2-isopropylmalate synthase (RefSeq)
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__PV4:5211056 Length = 523 Score = 369 bits (946), Expect = e-106 Identities = 218/512 (42%), Positives = 314/512 (61%), Gaps = 20/512 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQ+ A++T +KL+ A L +LGVD++E GFP +S DF +V+ IA Sbjct: 5 VIIFDTTLRDGEQALAASLTVKEKLQIALSLERLGVDVMEVGFPVSSPGDFESVQTIART 64 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 + N + ++R EKDI A ++L A++ R+ TFI+TS IH+E KL++S D Sbjct: 65 IKNSR--------VCALARALEKDIDAAAQSLSVAEQFRIHTFISTSTIHVESKLKRSFD 116 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 QVL+ A VK+AR D++F EDA R+ + L ++ IKAGA T+ IPDTVG Sbjct: 117 QVLDMAVGAVKYARRF-TDDVEFSCEDAGRTPIDNLCRMVEAAIKAGAKTINIPDTVGYT 175 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 +P E+G +I ++ P I+ A+++ HCH+DLGL+ AN+I ++GARQ+E T+NGIGER Sbjct: 176 VPSEFGGIIQNLFDRVPNIDQAVISVHCHDDLGLSVANSITAVQHGARQIECTVNGIGER 235 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGN S EE+ M + R + GL TGIN + I +TS +V + + +Q +KA+VGANAF Sbjct: 236 AGNCSLEEIAMIIATRKASL--GLETGINAKEIHRTSNLVSQLCNMPVQANKAIVGANAF 293 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 H SGIHQDG+LK + TYEI++PE IGL R + + + SGR +++R+EE+GY +D Sbjct: 294 THSSGIHQDGVLKSQNTYEIMTPESIGLNR---NNLNMTSRSGRHVIKHRMEEMGYGEQD 350 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEA-FNEQPIWKLGDLQV-TCGTVGFSTAT 442 +++ ++ F +A+KK ++ D DL ALV EA ++ + L L V + T G +TAT Sbjct: 351 YDMDTLYEAFLKLADKKGQVFDYDLEALVYVEAQAEDENHYGLQQLVVHSDSTQGQATAT 410 Query: 443 VKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEI 502 V L SIDG + G GPVD+AYKAI + Y L A +G DA + Sbjct: 411 VTL-SIDGKAVTEAATGNGPVDAAYKAIARASGCEINISSYQLSAKGQGQDALGQVDITA 469 Query: 503 SRGDTNHPVFSGTGGGTDVVVSSVDAYLSALN 534 D + F G G TDVV +S A + +N Sbjct: 470 KYHDQS---FHGVGLATDVVEASAAALIHVMN 498 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: 623 Number of extensions: 29 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: 523 Length adjustment: 35 Effective length of query: 505 Effective length of database: 488 Effective search space: 246440 Effective search space used: 246440 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