Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate PP_2336 PP_2336 aconitate hydratase 1
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Putida:PP_2336 Length = 862 Score = 1435 bits (3715), Expect = 0.0 Identities = 723/861 (83%), Positives = 772/861 (89%), Gaps = 2/861 (0%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT YRK LPGT LDYFD R A+EAI PGAY LPYTSRVLAENLVRRC+P L ASL Q Sbjct: 1 MNTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 +IE K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA KGGDPAQVNPVVP QLIVDH Sbjct: 61 LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE GGFD AF KNRAIEDRRNEDRFHFINWT+KAFKN+DVI GNGIMHQINLE+M Sbjct: 121 SLAVECGGFDPQAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIQPGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPV+H+ GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLP+I+GV Sbjct: 181 SPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPEIVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGK P ITATD+VLALTEFLR QKVV +YLEF GEGA ALTLGDRATISNM PE+GA Sbjct: 241 ELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMF IDQQT+DYL LTGRE +QVKLVETYAK GLW+D L AVY RTL FDLSSVVR Sbjct: 301 TAAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 +AGPSNPHARV TS+LAA+GI+G E PG MPDGAVIIAAITSCTNTSNPRNVIAAGL Sbjct: 361 NMAGPSNPHARVATSDLAAKGIAGSWEEVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 +ARNAN GLTRKPWVK+SLAPGSKAVQLYLEEA L ELE LGFGIV FACTTCNGMSG Sbjct: 421 IARNANKLGLTRKPWVKSSLAPGSKAVQLYLEEAGLEKELEQLGFGIVAFACTTCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE Sbjct: 481 ALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KDVLG+ DGK +RL +IWPSD EIDAV+ A+VKPEQFRKVY PMF + D G KV+PLY Sbjct: 541 KDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEEDRGPKVAPLY 599 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 DWRP STYIRRPPYWEGALAGERTL+GMRPLAVL DNITTDHLSPSNAIM+DSAAGEYL Sbjct: 600 DWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 659 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMA-IVDGKVKQGSLARIEPEGIVTR 723 KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM DG VKQGSLARIEPEG VTR Sbjct: 660 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRNDDGSVKQGSLARIEPEGKVTR 719 Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783 MWEAIETYM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM Sbjct: 720 MWEAIETYMQRKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 779 Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843 GVLPLEFK G +R T G+DG+E +DV+G+ PRA LT+++TR NGE +EVPVTCRLDTAE Sbjct: 780 GVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANGECLEVPVTCRLDTAE 839 Query: 844 EVSIYEAGGVLQRFAQDFLES 864 EVSIYEAGGVLQRFAQDFLE+ Sbjct: 840 EVSIYEAGGVLQRFAQDFLEA 860 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: 2236 Number of extensions: 90 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 867 Length of database: 862 Length adjustment: 42 Effective length of query: 825 Effective length of database: 820 Effective search space: 676500 Effective search space used: 676500 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: 56 (26.2 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