Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_081822814.1 P166_RS0110785 2-isopropylmalate synthase
Query= BRENDA::P9WQB3 (644 letters) >NCBI__GCF_000711315.1:WP_081822814.1 Length = 538 Score = 486 bits (1251), Expect = e-141 Identities = 260/536 (48%), Positives = 351/536 (65%), Gaps = 25/536 (4%) Query: 41 MPVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFD 100 M ++YRP V P L NR WP+R + +AP+W +VDLRDGNQAL PM+ +K +++D Sbjct: 1 MNFHKYRP---TVTP-DLPNRQWPNRRLTKAPIWVSVDLRDGNQALAKPMTVEQKLKLWD 56 Query: 101 LLVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSG 160 LV +G+K IE+GFPSASQ +FDF R +IE+ IPDDVT+QVL Q R LIERT++A +G Sbjct: 57 KLVSIGFKTIEIGFPSASQLEFDFTRRLIEENRIPDDVTVQVLVQAREHLIERTYEALAG 116 Query: 161 APRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESY 220 +A++H YN+TS +QR VF + E++ IA DGA E A +YP T W F+YSPES+ Sbjct: 117 VKQAVIHVYNTTSRVQRDKVFCKTKDEIKQIAVDGATWVQEYAKRYPETHWIFQYSPESF 176 Query: 221 TGTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESV 280 + TE ++A +VC AV +V PTP+ I NLP+TVE T+PN +AD IE+ ++ NRES Sbjct: 177 SQTETDFAVEVCQAVMDVWQPTPQNKCILNLPSTVESTSPNRFADQIEYFITHMQNRESA 236 Query: 281 ILSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQI 340 I+S+H HNDRG AVAAAEL AGADR+EG L GNGERTGN+ +VTL +NL+S G++P++ Sbjct: 237 IISVHTHNDRGCAVAAAELAILAGADRVEGTLLGNGERTGNMDVVTLAMNLYSEGINPEL 296 Query: 341 DFSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCD 400 +FSN D+ VE Q+ H RHP+ G VYTA+SGSHQDAI K L Sbjct: 297 NFSNPDDWIEVVEEVTQIETHIRHPWVGQAVYTAYSGSHQDAIRKCLAVQN--------- 347 Query: 401 VDDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQV 460 DD W V YLPIDP+D+ R YEA+IRVNSQSGK G A++++ ++GL+LP+ +Q +F+ V Sbjct: 348 -DDKPWDVAYLPIDPKDIQRDYEAIIRVNSQSGKAGAAFVLEQEYGLNLPKWVQQDFAPV 406 Query: 461 IQKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKI 520 Q AE T G VS K ++DAF E Y + H DG ++++ Sbjct: 407 AQNCAEST---DGVVSHKVLFDAFVEHY--RLNDSHSQLNHYKLDKQDG---KEHLSLEV 458 Query: 521 NGVETEISGSGNGPLAAFVHALAD-VGFDVAVLDYYEHAMSAGDDAQAAAYVEASV 575 NG + G GNG L+A +A + ++ VLDY EHAM G +A+A AY+ V Sbjct: 459 NGETWQ--GVGNGTLSALCNAWQNKTQNEIDVLDYAEHAMHQGKEAKAIAYIHVQV 512 Lambda K H 0.317 0.133 0.399 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: 804 Number of extensions: 30 Number of successful extensions: 4 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: 644 Length of database: 538 Length adjustment: 37 Effective length of query: 607 Effective length of database: 501 Effective search space: 304107 Effective search space used: 304107 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: 53 (25.0 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