Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate 8501897 DvMF_2612 pyruvate carboxyltransferase (RefSeq)
Query= curated2:Q8RCF9 (384 letters) >FitnessBrowser__Miya:8501897 Length = 455 Score = 191 bits (484), Expect = 5e-53 Identities = 122/372 (32%), Positives = 196/372 (52%), Gaps = 17/372 (4%) Query: 11 IVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKLGL 70 ++DTTLR+GEQ+ G + ++ R+ + L +G+ + EVG D + +A A++ Sbjct: 2 LLDTTLREGEQSFGTYLSMADRERVLRGLAAVGVPEAEVGWAGRE-DLTDMLALSARVAP 60 Query: 71 KASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRFAK 130 + AW R D++ ++ CG V + + SD H+ +L R +LD + + A+ Sbjct: 61 GLAAAAWCRCRPGDLRAAVACGASRVCVGVPVSDAHLARRLGLGRAALLDLLAATLAEAR 120 Query: 131 KEGV-YVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIKD 189 G+ +V+V EDASR D F+ A A GA R+R DTVG P + ++V+A++ Sbjct: 121 MLGIEHVTVGMEDASRADRAFVFAVACHAAAHGAHRVRLSDTVGLYTPLEVADVVRALRA 180 Query: 190 AVD-------------IEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAA 236 ++ + I H HND GMATANAL ++ GA V+V GLGERAG A Sbjct: 181 ELEGARQDDTAPRARRVSIGTHFHNDCGMATANALTALECGADCADVSVLGLGERAGVAR 240 Query: 237 LEEVVMALKYVYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDG 296 LEE+ AL V + + + R + VA A+ +P + G+++FA ESG+H G Sbjct: 241 LEELAAAL--VVRGRARFELAPLRALCGQVAQAASLSVPRHWPVAGRDIFAVESGLHAHG 298 Query: 297 ALKNPYTYEVFDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMA 356 ++P +E F P+ VG R++ +G+ SG AA+ E + +E ++ VR ++ Sbjct: 299 VRRDPSLFEPFPPELVGDSRRMGVGRKSGVAAVAAALAELSILPPPDELPAIVEAVRDLS 358 Query: 357 IQLKRPLFDKEL 368 L+RPL EL Sbjct: 359 ATLRRPLTPAEL 370 Lambda K H 0.318 0.135 0.379 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: 341 Number of extensions: 16 Number of successful extensions: 5 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: 384 Length of database: 455 Length adjustment: 32 Effective length of query: 352 Effective length of database: 423 Effective search space: 148896 Effective search space used: 148896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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