Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate RR42_RS05465 RR42_RS05465 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Cup4G11:RR42_RS05465 Length = 512 Score = 402 bits (1032), Expect = e-116 Identities = 237/512 (46%), Positives = 320/512 (62%), Gaps = 20/512 (3%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTTLRDGEQSPGA+MT +K+ ARQL +L VD+IEAGF +S DF A++ IA+ V Sbjct: 7 IFDTTLRDGEQSPGASMTREEKIRIARQLERLKVDVIEAGFAASSNGDFEAIRSIAQVVK 66 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + I ++R N++DIA A EALK A R+ TFIATS +HME KLR + DQV Sbjct: 67 DST--------ICSLARANDRDIARAAEALKPANSFRIHTFIATSALHMEKKLRMTPDQV 118 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 E A V+FAR DI+F ED +RSD +FL ++ VIK GATT+ +PDTVG A+P Sbjct: 119 FEQAIQAVRFARQF-TDDIEFSPEDGSRSDMDFLCRVLEGVIKEGATTINLPDTVGYAVP 177 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARY-GARQLEVTINGIGERA 265 Y LI ++ P + AI + HCHNDLG+A AN++ + GARQ+E TING+GERA Sbjct: 178 EGYAGLIRSVRERIPNSDKAIWSVHCHNDLGMAVANSLAAVKLGGARQVECTINGLGERA 237 Query: 266 GNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFL 325 GN S EEVVMA+ R + G++T I+ SK+V + +G +QP+KA+VGANAF Sbjct: 238 GNTSLEEVVMAVKTRRDYF--DMDVGVDTTQIVPASKLVSQITGFVVQPNKAVVGANAFA 295 Query: 326 HESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLK-D 384 H SGIHQDG+LK R TYEI+ ED+G + IVLGKLSGR A + RL+ELG +L+ + Sbjct: 296 HASGIHQDGVLKARDTYEIMRAEDVGW---SANKIVLGKLSGRNAFKQRLQELGIELESE 352 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVK 444 EV F +FK +A++K I D D+ A+VS+EA + ++ L T A V Sbjct: 353 GEVNAAFTRFKELADQKSEIFDEDIMAIVSDEAHDVNEHFRFISLSQHSETGERPHARV- 411 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 +F++DG+ G GPVD+ AI V A+LV Y++ AIT G A +V +S+ Sbjct: 412 VFNMDGNEVTGEGEGNGPVDATLHAIEGKVASGAELVLYSVNAITAGTQAQGEVTVRLSK 471 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 G + +G G D+V +S AYL+ALN + Sbjct: 472 GGR---IVNGVGTDPDIVAASAKAYLAALNKL 500 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: 600 Number of extensions: 30 Number of successful extensions: 9 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: 512 Length adjustment: 35 Effective length of query: 505 Effective length of database: 477 Effective search space: 240885 Effective search space used: 240885 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