Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate WP_084657418.1 N745_RS0109335 2-isopropylmalate synthase
Query= SwissProt::P42455 (616 letters) >NCBI__GCF_000526715.1:WP_084657418.1 Length = 539 Score = 491 bits (1264), Expect = e-143 Identities = 247/549 (44%), Positives = 363/549 (66%), Gaps = 25/549 (4%) Query: 53 LPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQMGFKEIEVGFPSA 112 LP+R WP+K++T AP W +VDLRDGNQAL PM+ E+K ++++ LV +GFK IE+GFPSA Sbjct: 14 LPNRQWPNKRLTQAPIWVSVDLRDGNQALAKPMTVEQKLKLWDKLVSIGFKTIEIGFPSA 73 Query: 113 SQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNVIVHFYNSTSILQR 172 SQ +FDF R +IE+ IPDDVT+QVLVQAREHLI+RT+EA EG K ++H YN+TS +QR Sbjct: 74 SQLEFDFTRRLIEENRIPDDVTVQVLVQAREHLIKRTYEALEGVKQAVIHVYNTTSRVQR 133 Query: 173 NVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFTGTEVEYAKEVVDAVVE 232 + VF + ++K++A A ++ A+ +P +NW +QYSPESF+ TE +YA EV AV++ Sbjct: 134 DKVFEKTQDEIKQMAVQGATWVQDYAKQHPTSNWIFQYSPESFSQTETDYAVEVCQAVMD 193 Query: 233 VMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSLHPHNDRGTGVGAA 292 V PTP+N I+NLP+TVE +PN +AD IE+ +L R+S I+S+H HNDRG V AA Sbjct: 194 VWQPTPQNKCILNLPATVESTSPNRFADQIEYFITHLQNRESTIISVHTHNDRGCAVAAA 253 Query: 293 ELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTDIRQIRSTVEYCNQ 352 EL +AGADR+EG L GNGERTGN+ +VTLA+N ++G++P+L+F++ VE Q Sbjct: 254 ELAILAGADRVEGTLLGNGERTGNMDIVTLAMNFYSEGINPELNFSNPDDWIEVVEEVTQ 313 Query: 353 LRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVSWEQLRDTEWEVPY 412 + RHP+ G V+TA+SGSHQDA+ K L Q W+V Y Sbjct: 314 IPTHIRHPWVGQAVYTAYSGSHQDAIRKCLTV-----------------QKDSNPWDVAY 356 Query: 413 LPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEFSTVVQNVTDAEGG 472 LPIDPKD+ RDYEA+IRVNSQSGK G A++++ ++GL +P+ +Q +F+ QN ++ G Sbjct: 357 LPIDPKDIQRDYEAIIRVNSQSGKAGAAFVLEQEYGLHLPKWVQQDFAPTAQNCAESTDG 416 Query: 473 EVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAELIHNGKDVTVDGRGNG 532 V+ K ++D F Y + + A+++++ + + +D L NG+ + G GNG Sbjct: 417 VVSHKILYDAFIKHY-----KLSESAIQLDHYKLDKQDGKEHLSLNVNGE--SWQGVGNG 469 Query: 533 PLAAYANALE-KLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNGRKVWGVGIAGSITYA 591 L+A NA + K ++++ +Y +HA G +A+A AY+ +V +K G+ + A Sbjct: 470 TLSALCNAWQNKTNQEIDVLDYAEHAMQQGKEAKAIAYIYVQVGDQKRIGIAMMEDSLSA 529 Query: 592 SLKAVTSAV 600 ++A+ SAV Sbjct: 530 MMQALISAV 538 Lambda K H 0.316 0.133 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: 857 Number of extensions: 33 Number of successful extensions: 3 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: 616 Length of database: 539 Length adjustment: 36 Effective length of query: 580 Effective length of database: 503 Effective search space: 291740 Effective search space used: 291740 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 (21.6 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