Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Ac3H11_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1140 Length = 980 Score = 613 bits (1580), Expect = e-179 Identities = 365/934 (39%), Positives = 528/934 (56%), Gaps = 109/934 (11%) Query: 37 KLPYTSRVLAENLVRRCE-----PEMLTASLKQIIESKQELDFPWFPARVVCHDILGQTA 91 +LP + R++ E+++R C+ PE + + ++++ + P+ +RVV D G Sbjct: 48 RLPVSIRIVLESVLRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPL 107 Query: 92 LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151 L DLA +R A G +P ++ P+VP L+VDHS+ +++ G K++ N +E +RN + Sbjct: 108 LADLAAMRSVAAKLGKNPKKIEPLVPVDLVVDHSIMIDHYG-KKNSLDLNMKLEFQRNRE 166 Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR-NGVAFPDTLVGTDSHTPHV 210 R+ F+ W +AF V+P G GI+HQ+NLE ++ +H R +GV +PDTLVGTDSHT + Sbjct: 167 RYEFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMI 226 Query: 211 DALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQ 270 + +GV+ GVGG+EAE+ MLG+ Y PD++G E+TG+ + G+TATD+VL +TE LR Sbjct: 227 NGIGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKH 286 Query: 271 KVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVK 330 KVV ++EFFGEG L L DRATI NM PE+GAT F +D++T+DY TGR +++ Sbjct: 287 KVVGKFVEFFGEGTRTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIE 346 Query: 331 LVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVRTIAGPSNPHARVPT-------SELA 382 E Y K GL+ L V Y + + DL SV ++AGP P R+ ++L Sbjct: 347 AFEAYFKAQGLFGVPLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLF 406 Query: 383 ARGISGEVENEPGLM-------PDGAVIIAAIT---SCTNTSNPRNVI------------ 420 ++ + N P + A ++A +T T PR+V+ Sbjct: 407 SQPAAHNGFNRPAELLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATA 466 Query: 421 -----AAGLLARNAN--------------------------AKGLTRKPWVK-------- 441 +A L AR A+ A GL K V+ Sbjct: 467 HAEARSATLPARGADPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPH 526 Query: 442 --TSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDL 499 TSLAPGS+ V YL E LLP LE LGF I G+ CTTC G +G L P + + + DL Sbjct: 527 IKTSLAPGSRIVTEYLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDL 586 Query: 500 YATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRL 559 AVLSGNRNF+ RIHP K FLASPPLVVAYAIAGT+ D+ + +G K GK + L Sbjct: 587 VCAAVLSGNRNFEARIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYL 646 Query: 560 INIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPL----YDWRPQSTYIRR 615 +IWPS E+ A++ ++K + FR Y + +K+ + Y W P STYI Sbjct: 647 GDIWPSSDEVHALLKFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTW-PASTYIAE 705 Query: 616 PPYW------EGA--LAGER----------TLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657 PP++ +GA +G R ++ G R +A+ GD+ITTDH+SP+ +I S Sbjct: 706 PPFFAQFALEKGANKASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESS 765 Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQGSLARI 715 AG++L + G+ + DFNSY RG+H R TFAN ++KN M DG ++G + Sbjct: 766 PAGQWLLQHGVQKADFNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVF 825 Query: 716 EPEGIVTR----MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEG 771 + EG + +++A YM + P ++ AG +YG GSSRDWAAKG +L G++A+VA Sbjct: 826 QNEGALQGEKMFIFDAAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARS 885 Query: 772 FERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVI--GSIAPRADLTVIITRKNGE 829 FERIHR+NLVGMGVLPL+FKAG++ T G+ G EV DV+ ++ P++D ++I R +G Sbjct: 886 FERIHRSNLVGMGVLPLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGT 945 Query: 830 RVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863 EV VT R+DT EV Y AGG+L + LE Sbjct: 946 VREVVVTLRIDTPIEVDYYRAGGILPFVLRQLLE 979 Lambda K H 0.318 0.136 0.397 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: 2096 Number of extensions: 113 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 867 Length of database: 980 Length adjustment: 43 Effective length of query: 824 Effective length of database: 937 Effective search space: 772088 Effective search space used: 772088 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: 57 (26.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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