Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate Synpcc7942_0903 Synpcc7942_0903 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:O27439 (419 letters) >FitnessBrowser__SynE:Synpcc7942_0903 Length = 861 Score = 111 bits (278), Expect = 7e-29 Identities = 116/452 (25%), Positives = 193/452 (42%), Gaps = 58/452 (12%) Query: 4 TVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVVI 63 T+++K++ RA G V G + + D TGP++ + + + + + ++ Sbjct: 373 TLAQKMVGRACGLPGVRPGTSCEPIMTTVGSQDTTGPMTRDEMKELA-CLGFSADLVMQS 431 Query: 64 FDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTDS 123 F H + H + DF+ ++G +G+ H L ++P V G DS Sbjct: 432 FCHTAAYPKPVDIKTHKTLPDFIAQRG-GVALKPGDGIIHSWLNRM--LLPDTVGTGGDS 488 Query: 124 HTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVIL 179 HT F GI GS +A A G + +PE++ G L+ + +DV+ Sbjct: 489 HT-------RFPLGISFPAGSGLVAFAAAIGAMPLDMPESVLVRFTGSLQPGITLRDVVN 541 Query: 180 NIIGRVGADGATYMACE-----FAG-----ETVAEMSVSDRMVLSNMAIEMGGKTGIVEP 229 I + G ++ E F+G E + ++ + L++ E ++ Sbjct: 542 AIPYQAIQQGLLTVSKENKVNVFSGRIMEIEGLPDLKLEQAFELTDATAERSCAGSTIKL 601 Query: 230 DEKTL------------NYVRR------------RSGKPW----RVFKTDPDAPSLSVME 261 E T+ N + R R + W ++ D DA +V+E Sbjct: 602 SEDTVAEYLRSNVALMKNMIARGYEDSRTLARRIRQMEDWLANPQLLSADEDAEYAAVIE 661 Query: 262 VDVSDL-EPQVACPHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDAAAILKNRKVS 320 +++ +L EP +ACP++ DNVK ++EV G I ++F+GSC + R AA +L+ Sbjct: 662 INLDELTEPILACPNDPDNVKKLSEVAGDPIHEIFIGSCMT-NIGHYRAAAKVLEGEGQV 720 Query: 321 DSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLVGPGEVSLSTS 380 R+ + P +R R +EG F AGA + P C C+G V STS Sbjct: 721 GG-RLWICPPTRMDEDRLKEEGYYSTFAAAGARLEVPGCSLCMGNQ-ARVADNTTVFSTS 778 Query: 381 NRNFRGRQGSPEAEVYLSSAAVAAASAVKGSI 412 RNF R G A+VYL SA +AA A+ G I Sbjct: 779 TRNFNNRMGK-GAQVYLGSAELAAVCALLGRI 809 Lambda K H 0.318 0.135 0.396 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: 790 Number of extensions: 49 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 419 Length of database: 861 Length adjustment: 37 Effective length of query: 382 Effective length of database: 824 Effective search space: 314768 Effective search space used: 314768 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: 53 (25.0 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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