Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate Dsui_2205 Dsui_2205 aconitate hydratase 2
Query= BRENDA::P81291 (424 letters) >FitnessBrowser__PS:Dsui_2205 Length = 865 Score = 126 bits (316), Expect = 3e-33 Identities = 126/463 (27%), Positives = 206/463 (44%), Gaps = 67/463 (14%) Query: 2 GMTIVEKILAKASGKKE---VSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPE 58 G ++ +K++ +A G E + PG + D TGP+T + LK+ ++ + Sbjct: 383 GYSLAQKMVGRACGLPEGKGILPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLG-FSAD 441 Query: 59 KIVILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVV 118 ++ F H + H + F+ +G +GV H L + P V Sbjct: 442 LVMQSFCHTAAYPKLVDVRMHRELPSFISTRGGVALRP-GDGVIHSWLNRL--LLPDTVG 498 Query: 119 VGADSHTCTHGAFGAFATGI----GSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTS 174 G DSHT F GI GS +A ATG + +PE++ G +QP +T Sbjct: 499 TGGDSHT-------RFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITL 551 Query: 175 KDVILSII------GEVGVDGATYKACQFGG----ETVKKMSIASRMTMTNMAIEMGG-- 222 +D++ +I G + V+ K G E + + + +++ A E Sbjct: 552 RDLVNAIPLYAIKQGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSDAAAERSAAA 611 Query: 223 ------KTGIIE-----------------PDEKTIQYVKEAMKK---HGTERPFEVIKGD 256 K I+E D +T++ +AM++ +GT ++K D Sbjct: 612 CAIALNKEPIVEYLRSNITLMKWMIAEGYQDARTLKRRIKAMEEWIANGT-----LLKAD 666 Query: 257 EDAEFAEVYEIE-ADKIEPVFACPHNVDNVKQAREVAGKPIDQVFIGSCTNGRLEDLRMA 315 DA++A V EI+ AD EP+ ACP++ D+VK EVAG ID+VFIGSC + R A Sbjct: 667 TDAQYAAVIEIDLADVKEPIVACPNDPDDVKVLSEVAGDKIDEVFIGSCMT-NIGHFRAA 725 Query: 316 IKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTNPSCSACMGSLYGV 375 K+++ I R+ + P ++ + L +EG K G + P CS CMG+ Sbjct: 726 GKVLDGKSDI--PTRLWIAPPTKMDALILTEEGYYSVLGKAGARMEMPGCSLCMGN-QAQ 782 Query: 376 LGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGEL 418 + G +STS RNF R G ++ +YL S AA C++ G++ Sbjct: 783 IRKGSTAMSTSTRNFPNRLG-IDTRVYLGSAELAAMCSLLGKI 824 Lambda K H 0.318 0.136 0.400 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: 845 Number of extensions: 46 Number of successful extensions: 7 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: 424 Length of database: 865 Length adjustment: 37 Effective length of query: 387 Effective length of database: 828 Effective search space: 320436 Effective search space used: 320436 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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