Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate 14264 b0118 aconitate hydratase (NCBI)
Query= curated2:O27439 (419 letters) >FitnessBrowser__Keio:14264 Length = 865 Score = 111 bits (278), Expect = 8e-29 Identities = 114/457 (24%), Positives = 202/457 (44%), Gaps = 61/457 (13%) Query: 4 TVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVVI 63 ++++K++ RA G + G + + D TGP++ + + + + + ++ Sbjct: 383 SLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPMTRDELKDLA-CLGFSADLVMQS 441 Query: 64 FDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTDS 123 F H H + DF+ +G + +GV H L ++P V G DS Sbjct: 442 FCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRP-GDGVIHSWLNRM--LLPDTVGTGGDS 498 Query: 124 HTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVIL 179 HT F GI GS +A ATG + +PE++ +GK++ + +D++ Sbjct: 499 HT-------RFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVH 551 Query: 180 NIIGRVGADGATYMACE-----FAG-----ETVAEMSVSDRMVLSNMAIEMGG------- 222 I G + + F+G E + ++ V L++ + E Sbjct: 552 AIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKL 611 Query: 223 -KTGIVE-----------------PDEKTLNYVRRRSG-KPW----RVFKTDPDAPSLSV 259 K I+E D +TL RR G + W + + D DA +V Sbjct: 612 NKEPIIEYLNSNIVLLKWMIAEGYGDRRTLE--RRIQGMEKWLANPELLEADADAEYAAV 669 Query: 260 MEVDVSDLEPQVAC-PHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDAAAILKNRK 318 +++D++D++ + C P++ D+ +P++ V+G +ID+VF+GSC + R A +L K Sbjct: 670 IDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMT-NIGHFRAAGKLLDAHK 728 Query: 319 VSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLVGPGEVSLS 378 R+ V P +R + +EG +F +GA + P C C+G V G +S Sbjct: 729 GQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQ-ARVADGATVVS 787 Query: 379 TSNRNFRGRQGSPEAEVYLSSAAVAAASAVKGSITHP 415 TS RNF R G+ A V+L+SA +AA +A+ G + P Sbjct: 788 TSTRNFPNRLGT-GANVFLASAELAAVAALIGKLPTP 823 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: 810 Number of extensions: 46 Number of successful extensions: 5 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: 865 Length adjustment: 37 Effective length of query: 382 Effective length of database: 828 Effective search space: 316296 Effective search space used: 316296 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 Jul 25 2024. The underlying query database was built on Jul 25 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