Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate Ac3H11_530 2-isopropylmalate synthase (EC 2.3.3.13)
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_530 Length = 512 Score = 406 bits (1044), Expect = e-118 Identities = 240/513 (46%), Positives = 325/513 (63%), Gaps = 21/513 (4%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTTLRDGEQSPGA+MT +KL ARQL +L VD+IEAGF +S DF AV+ IA + Sbjct: 7 IFDTTLRDGEQSPGASMTKDEKLRIARQLERLKVDVIEAGFAASSNGDFEAVQAIANAIK 66 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + I +SR N++DI+ A EAL+ A R+ TFIATS +HME KLR + +QV Sbjct: 67 DST--------ICSLSRANDRDISRAAEALRGANSARIHTFIATSALHMEKKLRMTPEQV 118 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 LE A+ V+FAR+L DI+F ED RSD +FL ++ VI GATT+ +PDTVG A+P Sbjct: 119 LEQAKQSVRFARNL-VADIEFSPEDGYRSDPDFLCRVLEAVITEGATTINVPDTVGYAVP 177 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARY-GARQLEVTINGIGERA 265 YG I ++ P + AI + HCHNDLG+A AN++ G + GARQ+E TING+GERA Sbjct: 178 ELYGNFIKTLRERIPNSDKAIWSVHCHNDLGMAVANSLAGVKIGGARQVECTINGLGERA 237 Query: 266 GNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFL 325 GN S EE+VMA+ R GL I+T+HI+ S+MV + +G +QP+KA+VGANAF Sbjct: 238 GNCSLEEIVMAVKTR--KDYFGLDLAIDTQHIVAASRMVSQTTGFVVQPNKAVVGANAFA 295 Query: 326 HESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKL-KD 384 H SGIHQDG+LK R TYEI+ ED+G + IVLGKLSGR A + RL+ELG +L + Sbjct: 296 HASGIHQDGVLKARDTYEIMRAEDVGW---SANKIVLGKLSGRNAFKQRLQELGVQLDSE 352 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFN-EQPIWKLGDLQVTCGTVGFSTATV 443 TE+ F +FK +A++K I D D+ ALVS+E+ E+ + L T A + Sbjct: 353 TEINVAFAKFKELADRKSEIFDEDILALVSDESVTAEKEQYGFVSLFQQSETGEQPRARI 412 Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503 +F++DG S G GPVD++ KAI VK A++V Y++ AI+ ++ +V + Sbjct: 413 -VFTVDGQEVRGESDGNGPVDASLKAIESHVKSGAEMVLYSVNAISGSTESQGEVTVRLQ 471 Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 V +G G D+VV+S AYLSALN + Sbjct: 472 NSGR---VVNGVGADPDIVVASAKAYLSALNKL 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: 600 Number of extensions: 21 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