Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate Echvi_2061 Echvi_2061 Isopropylmalate/homocitrate/citramalate synthases
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__Cola:Echvi_2061 Length = 504 Score = 251 bits (640), Expect = 5e-71 Identities = 164/496 (33%), Positives = 265/496 (53%), Gaps = 17/496 (3%) Query: 9 DTTLRDGEQTPGVSLTVEEKVEIARKL-DEFGVDTIEAGFPVASEGEFEAVRAI---AGE 64 DTTLRDGEQT GVS EK++IA+ L +E VD IE SEGE E V+ I A E Sbjct: 2 DTTLRDGEQTSGVSFLPSEKLQIAKLLLEELRVDRIEVASARVSEGELEGVKKITHWAAE 61 Query: 65 E--LDA-EICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALERAIEG 121 + LD E+ G +D +A +++ S HL ++L+ + E + Sbjct: 62 KGYLDCVEVLGFVD-TPASVDWLTEAGAKVLNLLTKGSLNHLTHQLKKTPVEHFAAIEKC 120 Query: 122 VEYASDHGVTVEFSAED---ATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPPEMYR 178 + YA++ G++V ED R RDY LE+ + RV +PDT+G++ P E+ Sbjct: 121 IHYANEKGISVNVYLEDWSSGMRHSRDYTLELIAFLADQNVKRVMLPDTLGLLKPAEVAE 180 Query: 179 LTAEVVDAV-DVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNASLEQVV 237 V + +V H HND+ ++VAN + A+ G +H TVNG+GERAGNA LE VV Sbjct: 181 YVGLVSEQFPEVHFDFHAHNDYDLSVANVMEAINHGISGIHTTVNGLGERAGNAPLESVV 240 Query: 238 MALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHGVIKKA 297 L ++L+V+ + +S+LVE+ +G+ +P N P+VGEN F +GIH+ G KK Sbjct: 241 ATLSDFTTVKLNVQENKIYRISKLVEQFSGLHIPSNKPVVGENVFTQTAGIHADGDNKKN 300 Query: 298 ETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLDEIVRRVKELGDKGKR 357 + + PE G R+ LGK +G+ I K L E+GI++ E+L ++ +++ ELGD+ +R Sbjct: 301 LYFNDLLPERFGRTRKYALGKTSGKANILKNLLELGIKLEPEELSKVTQKIIELGDRKER 360 Query: 358 VTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTASVRVYLDGEEHEAASTGVG 417 VT +DL I DV+ + + + +E + PT +++ + +EA ++G G Sbjct: 361 VTTEDLPYIISDVL-QNNSIKKDISIEGYHMTHSKGLKPTVQLKLKFKDQFYEAHASGNG 419 Query: 418 SVDAAIRALREAIEELGMDV-ELKEYRLEAITGG-TDALAEVTVRLEDEDGNVTTARGAA 475 D+ + AL++ + L + +L ++ + GG TDA E + + G + +G Sbjct: 420 QFDSFMLALQKIYKSLNKKLPKLTDFSVSIPPGGKTDAFVETVITW--DYGRIIKTKGLD 477 Query: 476 EDIVMASVKAFVRGVN 491 D +A++ A + +N Sbjct: 478 SDQTVAAMMATEKMLN 493 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: 531 Number of extensions: 20 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: 504 Length adjustment: 34 Effective length of query: 465 Effective length of database: 470 Effective search space: 218550 Effective search space used: 218550 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