Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate WP_019557799.1 F612_RS0110870 2-isopropylmalate synthase
Query= SwissProt::P42455 (616 letters) >NCBI__GCF_000381085.1:WP_019557799.1 Length = 560 Score = 473 bits (1216), Expect = e-137 Identities = 250/564 (44%), Positives = 356/564 (63%), Gaps = 35/564 (6%) Query: 52 SLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQMGFKEIEVGFPS 111 ++P+R WP+ +T AP W +VDLRDGNQAL +PM+ E+K +++ LV +GFK IEVGFPS Sbjct: 20 NMPNRQWPNNVLTKAPIWASVDLRDGNQALANPMTIEQKLTLWKQLVALGFKTIEVGFPS 79 Query: 112 ASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNVIVHFYNSTSILQ 171 ASQ +FDF+R +I+ +IPDDVTIQVLVQAREHLI+RT+EA G K +VH YN+TSI+Q Sbjct: 80 ASQIEFDFIRRLIDDNLIPDDVTIQVLVQAREHLIQRTYEALSGVKQAVVHVYNTTSIVQ 139 Query: 172 RNVVFRMDKVQVKKLATDAAELIKTIA----QDYPDTNWRWQYSPESFTGTEVEYAKEVV 227 R VF K +++ +A A ++ A + P + W +QYSPESF+ TE +YA V Sbjct: 140 RENVFEKSKDEIRAMAVQGARWVQEYALKASEINPHSKWIFQYSPESFSQTETDYAVSVC 199 Query: 228 DAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSLHPHNDRGT 287 AV++V PTP N I+NLP+TVE +PN +AD +E+ +L+ R+S+++S+H HNDRG Sbjct: 200 QAVMDVWQPTPNNKCILNLPATVESSSPNRFADQVEYFINHLSNRESVLISIHTHNDRGC 259 Query: 288 GVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTDIRQIRSTV 347 V AAEL +AGADRIEG L GNGERTGN+ +VTLA+N+ ++G+DP LD + V Sbjct: 260 AVAAAELSLLAGADRIEGTLLGNGERTGNMDIVTLAMNLFSEGIDPLLDLSQPNDWIPVV 319 Query: 348 EYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVSWEQLRDTE 407 E Q++ RHP+ G+ V+TA+SGSHQDA+ K L +Q D Sbjct: 320 EAVTQIKTHPRHPWVGEDVYTAYSGSHQDAIRKCL-----------------IKQQSDQP 362 Query: 408 WEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEFSTVVQNVT 467 W V YLPIDPKD+GRDYEA+IRVNSQSGK G A+++ ++GL +P+ MQ++F+ + Q + Sbjct: 363 WNVAYLPIDPKDIGRDYEAIIRVNSQSGKAGSAFVLAQEYGLSLPKWMQLDFAPIAQQLA 422 Query: 468 DAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAELIHNGKDVTVD 527 + +GG +N K ++ FA Y +E + + + Q + E L NG+ T Sbjct: 423 EKQGGVINHKELYSAFAKHYC-----IEDDGIVLNHYQLDREGDVEKLSLDVNGE--TWQ 475 Query: 528 GRGNGPLAAYANA-LEKLGIDVEIQEYNQHAR------TSGDDAEAAAYVLAEVNGRKVW 580 G G+G ++A +A ++ G V++ +Y +HA G +A A AYV +V G K Sbjct: 476 GVGSGTISALCDAWQQRTGQVVDVIDYAEHAMHITSNGKEGKNANAMAYVYLQVGGIKSV 535 Query: 581 GVGIAGSITYASLKAVTSAVNRAL 604 GV + A + AV + L Sbjct: 536 GVALEKDSVRAMVLAVIKGLYSVL 559 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: 896 Number of extensions: 53 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: 560 Length adjustment: 37 Effective length of query: 579 Effective length of database: 523 Effective search space: 302817 Effective search space used: 302817 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