Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_041099915.1 SUTH_RS13435 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000828635.1:WP_041099915.1 Length = 512 Score = 418 bits (1074), Expect = e-121 Identities = 243/512 (47%), Positives = 329/512 (64%), Gaps = 20/512 (3%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTTLRDGEQSPGA+MT +KL ARQL ++ VD+IEAGFP AS DF AV+ +AE + Sbjct: 8 IFDTTLRDGEQSPGASMTKEEKLRIARQLERMRVDVIEAGFPAASNGDFEAVRAVAETIK 67 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + + G+ R +KDIA A EA+K AK R+ TFIATSPIHME KLR S D V Sbjct: 68 DST--------VAGLCRAFDKDIARALEAVKPAKSGRIHTFIATSPIHMEKKLRMSPDDV 119 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 L A++ V+FAR+ G D++F EDA RSD +FL +I VIK GA+T+ IPDTVG +P Sbjct: 120 LVAAQHAVRFARN-GIGDVEFSCEDAGRSDLDFLCRIIEAVIKEGASTINIPDTVGYNVP 178 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGERAG 266 +Y + I ++ P + + + HCHNDLGLA AN++ GARQ+E TING+GERAG Sbjct: 179 EQYAERIRQLRERIPNSDKVVWSVHCHNDLGLAVANSLAAVMAGARQVECTINGLGERAG 238 Query: 267 NASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFLH 326 NA+ EE+VMA+ R D+ + T I+T I+ SKMV +G +QP+KA+VGANAF H Sbjct: 239 NAALEEIVMAVHTRQ-DVFPCI-TRIDTTQIVAASKMVSSITGFPVQPNKAIVGANAFAH 296 Query: 327 ESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKDTE 386 ESGIHQDG+LKHR TYEI+ ED+G + +VLGK SGR A + RL+ELG +++ + Sbjct: 297 ESGIHQDGVLKHRETYEIMRAEDVGW---NANKLVLGKHSGRTAFKARLKELGIEVESEQ 353 Query: 387 VEGV-FWQFKAVAEKKKRITDTDLRALVSNEAF-NEQPIWKLGDLQVTCGTVGFSTATVK 444 V V F FK +A+KK I D DL AL+S+E + +KL T A + Sbjct: 354 VLNVAFTHFKELADKKHEIFDEDLHALMSDEMVPPDDEHYKLVSSMFHSETGEAPQAKLT 413 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 L S G+ A S G+GPVD+ +KAI + ++L+ Y++ AIT G DA +V +S+ Sbjct: 414 L-SAGGTEQHAASSGSGPVDATFKAIESVAASGSELLLYSVNAITTGTDAQGEVTVRLSK 472 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 + + +G G TD+VV+S AY++ALN + Sbjct: 473 ---DGRIVNGQGADTDIVVASAKAYINALNKL 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: 615 Number of extensions: 27 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 10 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