Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate 351386 BT1858 2-isopropylmalate synthase (NCBI ptt file)
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__Btheta:351386 Length = 499 Score = 251 bits (642), Expect = 3e-71 Identities = 172/501 (34%), Positives = 265/501 (52%), Gaps = 21/501 (4%) Query: 9 DTTLRDGEQTPGVSLTVEEKVEIARKL-DEFGVDTIEAGFPVASEGEFEAVRAIAGEELD 67 DTTLRDGEQT GVS EK+ IAR L ++ VD +E SEGEFEAV+ I Sbjct: 2 DTTLRDGEQTSGVSFVPHEKLMIARLLLEDLKVDRVEVASARVSEGEFEAVKMICDWAAR 61 Query: 68 AEICGLARCVKGDIDAAIDAD----VDC--VHVFIATSDIHLRYKLEMSREEALERAIEG 121 + V G +D D C +++ S H +L+ + EE + I Sbjct: 62 RNLLQKVE-VLGFVDGHTSVDWIQRTGCRVINLLCKGSLKHCTQQLKKTPEEHIADIINV 120 Query: 122 VEYASDHGVTVEFSAEDATRTDRD---YLLEVYKATVEAGADRVNVPDTVGVMTPPEMYR 178 V YA + + V ED + +D Y+ ++ + R +PDT+G++ P ++ Sbjct: 121 VHYADEQDIGVNVYLEDWSNGMKDSPEYVFQLMDGLKQTSIRRYMLPDTLGILNPLQVIE 180 Query: 179 LTAEVVDAV-DVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNASLEQVV 237 ++ + H HND+ +AV+N LAAV +G +H T+NG+GERAGNA L V Sbjct: 181 YMRKMKKRYPNTHFDFHAHNDYDLAVSNVLAAVLSGVRGLHTTINGLGERAGNAPLSSVQ 240 Query: 238 MALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHGVIKKA 297 LK ++ ++ L ++SR+VE +G+V+P N PIVGEN F +G+H+ G K Sbjct: 241 AILKDHFNAMTNIDESRLNDVSRVVESYSGIVIPANKPIVGENVFTQVAGVHADGDNKNN 300 Query: 298 ETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLDEIVRRVKELGDKGKR 357 + PE G +R LGK +G+ I+K LE++G+E+ E+ + ++ R+ ELGDK + Sbjct: 301 LYCNDLLPERFGRKREYALGKTSGKANIRKNLEDLGLELDEDAMRKVTERIIELGDKKEL 360 Query: 358 VTEDDLEAIARDVV--GEVPESEAAVKLEEIAVMTGNKFTPTASVRVYLDGEEHEAASTG 415 VT++DL I DV+ G + E VKL+ V + P A++++ ++G+E+E +S+G Sbjct: 361 VTQEDLPYIVSDVLKHGAIGEK---VKLKSYFVNLAHGLKPMATLKIEINGKEYEESSSG 417 Query: 416 VGSVDAAIRALREAIE-ELGMDVE-LKEYRLEAITGG-TDALAEVTVRLEDEDGNVTTAR 472 G DA +RALR+ + LG L Y + GG TDA + TV + D V R Sbjct: 418 DGQYDAFVRALRKIYKVTLGRKFPMLTNYAVSIPPGGRTDAFVQ-TVITWNYDEQVFRTR 476 Query: 473 GAAEDIVMASVKAFVRGVNRL 493 G D A++KA ++ +N L Sbjct: 477 GLDADQTEAAIKATMKMLNLL 497 Lambda K H 0.315 0.133 0.364 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: 524 Number of extensions: 21 Number of successful extensions: 6 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: 499 Length of database: 499 Length adjustment: 34 Effective length of query: 465 Effective length of database: 465 Effective search space: 216225 Effective search space used: 216225 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 (21.5 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