Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate GFF2264 Psest_2309 aconitate hydratase 2
Query= BRENDA::P81291 (424 letters) >FitnessBrowser__psRCH2:GFF2264 Length = 875 Score = 121 bits (304), Expect = 7e-32 Identities = 127/469 (27%), Positives = 205/469 (43%), Gaps = 78/469 (16%) Query: 2 GMTIVEKILAKASGKKE---VSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPE 58 G T+ +K++ +A G E V PG + D TGP+T + LK+ ++ + Sbjct: 387 GFTLAQKMVGRACGLPEGKGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLG-FSAD 445 Query: 59 KIVILFDHQVPADS-IKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEV 117 ++ F H I +H L + G+ +G+ H L + P V Sbjct: 446 LVMQSFCHTAAYPKPIDVNTHHTLPDFIMNRSGVSLRPG--DGIIHSWLNRM--LLPDTV 501 Query: 118 VVGADSHTCTHGAFGAFATGI----GSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVT 173 G DSHT F GI GS +A ATG + +PE++ G +QP +T Sbjct: 502 GTGGDSHT-------RFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGQMQPGIT 554 Query: 174 SKDVILSIIGEVGVDGATYKACQFGGETVKK-------------------MSIASRMTMT 214 +D++ +I Y A Q G TV+K +++ ++ Sbjct: 555 LRDLVHAI---------PYYAIQQGLLTVEKKGKKNIFSGRILEIEGLNQLTVEQAFELS 605 Query: 215 NMAIEMGGKTGIIE-PDEKTIQYVKEAM--------KKHGTERPFE-------------- 251 + + E I+ P++ +Y+K + + +G R E Sbjct: 606 DASAERSAAGCTIKLPEDSIAEYLKSNITMLRWMISEGYGDARTLERRAQAMEAWLADPK 665 Query: 252 VIKGDEDAEFAEVYEIE-ADKIEPVFACPHNVDNVKQAREVAGKPIDQVFIGSCTNGRLE 310 +++ D+DAE+A V EI+ A+ EPV P++ D+ + VAG+ ID+VFIGSC + Sbjct: 666 LLEADKDAEYAAVIEIDLAEVKEPVLCAPNDPDDARLLSTVAGEKIDEVFIGSCMT-NIG 724 Query: 311 DLRMAIKIIEK-HGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTNPSCSACM 369 R A K+++K GGI R+ + P ++ + + +EG + K G + P CS CM Sbjct: 725 HFRAAGKLLDKVKGGI--PTRLWLAPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCM 782 Query: 370 GSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGEL 418 G+ V G VSTS RNF R G +YLAS AA ++ G+L Sbjct: 783 GNQARV-QTGSTVVSTSTRNFPNRLGD-ATNVYLASAELAAVASIIGKL 829 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: 853 Number of extensions: 50 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 424 Length of database: 875 Length adjustment: 37 Effective length of query: 387 Effective length of database: 838 Effective search space: 324306 Effective search space used: 324306 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 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