Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate Ac3H11_3150 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= curated2:O27439 (419 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3150 Length = 866 Score = 95.5 bits (236), Expect = 6e-24 Identities = 118/460 (25%), Positives = 193/460 (41%), Gaps = 75/460 (16%) Query: 4 TVSEKILARASGKDR---VEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKI 60 T+++K++ RA G V G + + D TGP++ + + + + + + Sbjct: 383 TLAQKMVGRAVGLPEGQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLA-CLGFSADLV 441 Query: 61 VVIFDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVG 120 + F H + H + F+ +G +GV H L ++P V G Sbjct: 442 MQSFCHTAAYPKPVDVKTHRELPAFISNRGGVALRP-GDGVIHSWLNRL--LLPDTVGTG 498 Query: 121 TDSHTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKD 176 DSHT F GI GS +A ATG + +PE++ +G ++ V +D Sbjct: 499 GDSHT-------RFPIGISFPAGSGLVAFGAATGVMPLDMPESILVRFKGDMQPGVTLRD 551 Query: 177 VI-----------LNIIGRVGADGATYMACEFAG-----ETVAEMSVSDRMVLSNMAIEM 220 ++ L + + G A F+G E + ++ V LS+ + E Sbjct: 552 LVHAIPLYAIKAGLLTVAKAGKINA------FSGRILEIEGLPDLKVEQAFELSDASAER 605 Query: 221 G--GKTGIVEP-----------------------DEKTLNYVRRRSGKPWR----VFKTD 251 G T + P D KTL R + W + + D Sbjct: 606 SAAGCTIKLNPEPIKEYLTSNIVLMKNMIADGYADAKTLQR-RIEKVEAWLAKPDLLEAD 664 Query: 252 PDAPSLSVMEVDVSDL-EPQVACPHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDA 310 DA +V+E+D++D+ EP V CP++ D+ K ++EV GT+ID+ F+GSC + R A Sbjct: 665 KDAEYAAVIEIDLADIKEPIVCCPNDPDDAKFLSEVSGTKIDEAFIGSCMT-NIGHFRAA 723 Query: 311 AAILKNRKVSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLV 370 A +L ++ V++ V P ++ + EG F AGA P C C+G V Sbjct: 724 AKLLGGQR-DIPVKLWVAPPTKMDESELIKEGHYAAFGTAGARTEMPGCSLCMGNQ-AQV 781 Query: 371 GPGEVSLSTSNRNFRGRQGSPEAEVYLSSAAVAAASAVKG 410 G +STS RNF R G V+L SA +AA ++ G Sbjct: 782 REGATVISTSTRNFPNRLGK-NTNVFLGSAELAAIASRLG 820 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: 778 Number of extensions: 43 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: 866 Length adjustment: 37 Effective length of query: 382 Effective length of database: 829 Effective search space: 316678 Effective search space used: 316678 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 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