Align 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate H281DRAFT_04763 H281DRAFT_04763 hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= curated2:C4XPA8 (513 letters) >FitnessBrowser__Burk376:H281DRAFT_04763 Length = 327 Score = 80.1 bits (196), Expect = 1e-19 Identities = 97/318 (30%), Positives = 139/318 (43%), Gaps = 51/318 (16%) Query: 1 MSD-DNRVYIFDTTLRDGEQSPGATMTREEKVRMARQLETLGVDIIE-AGFPAAS----E 54 MSD RV + + +RDG QS TM E K R GV +E A F A Sbjct: 1 MSDIRERVVVTEVGMRDGLQSIAQTMPTESKRRWIDAAYAAGVRHMEVASFVPAKLLPQM 60 Query: 55 GDFQAVSAIAAAVKTPVVAALCRALASDIDRGFEAIKGAQR------RRIHTFLATSELH 108 D V A A + +V AL L KGAQR RI ++ S H Sbjct: 61 ADADEVIAHALGYRDLIVTALVPNL-----------KGAQRALEAGVHRIVAPISVSAAH 109 Query: 109 MQHKLNKTPTQVLDMIEA---AVSHAASKGVE-VQFSAEDAS-------RSEPAFLVAAC 157 + KTP +++D+ A A+ A + G V+ A ++ + P +AA Sbjct: 110 SLANVRKTPAEMIDVFAAMREAIDGAPAAGTRRVELIAGLSTVFGCTLQGAVPYEDIAAI 169 Query: 158 ER-AINAGATILNIPDTVGYAQPAEFAELIRHLMTTVRG-AGGVTFAVHCHNDLGLAVAN 215 R A+ AGA ++ + DT G A P + E+I VRG AG ++H H+ GLA+AN Sbjct: 170 ARDAVRAGADVIALGDTTGEATPRQVGEIIE----VVRGVAGDKLRSLHLHDTRGLALAN 225 Query: 216 TLAALHAGARQAEVTLSGIG------ERAGNASLEQVVMGLNTRPNYYNLTTGIVTEELF 269 TL L G R+ + +L+G+G GN + E +V L + TGI L Sbjct: 226 TLVGLQHGIREFDASLAGLGGCPHAPGATGNVNTEDLVFMLES----MGYETGIDLTRLI 281 Query: 270 PSCRRLSGII-GQPIPPY 286 S L+ + G+P+ Y Sbjct: 282 ASRAVLADALPGEPLYGY 299 Lambda K H 0.319 0.133 0.376 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: 351 Number of extensions: 15 Number of successful extensions: 2 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: 513 Length of database: 327 Length adjustment: 31 Effective length of query: 482 Effective length of database: 296 Effective search space: 142672 Effective search space used: 142672 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 (21.8 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