Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_043530831.1 JH15_RS12220 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000759345.1:WP_043530831.1 Length = 866 Score = 1412 bits (3656), Expect = 0.0 Identities = 695/861 (80%), Positives = 767/861 (89%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT++RKPLPGT+LD+FDTR A+EAI PGAY +LPYTSRVLAENLVRRC+P LT SLKQ Sbjct: 1 MNTEFRKPLPGTSLDHFDTRAAVEAILPGAYDRLPYTSRVLAENLVRRCDPAALTDSLKQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 I+E K++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDPA+VNPVVPTQLIVDH Sbjct: 61 IVERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE+ GF+ DAF KNRAIEDRRN+DRFHFINWT+ AF+N+DVIP GNGIMHQINLE+M Sbjct: 121 SLAVEHAGFESDAFEKNRAIEDRRNDDRFHFINWTKLAFENVDVIPPGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPV+ R+GVAFPDT VGTDSHTP VDALGVI++GVGGLEAESVMLGRAS MRLPDI+GV Sbjct: 181 SPVVQKRDGVAFPDTCVGTDSHTPMVDALGVISVGVGGLEAESVMLGRASMMRLPDIVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTG+ QPGIT+TD+VLALT+FLR ++VV +YLEFFGEGA ALT+GDRATISNMTPE+GA Sbjct: 241 ELTGRLQPGITSTDMVLALTDFLRRERVVGAYLEFFGEGARALTVGDRATISNMTPEYGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMFYID+QT+DYL LTGR+ +QV LVETYAK AGLW+D L A Y R L FDLSSV R Sbjct: 301 TAAMFYIDEQTIDYLKLTGRDEDQVTLVETYAKEAGLWADCLADADYERVLTFDLSSVPR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 T+AGPSNPHA +PT+ELA RGISG V+++ G MPDGAVIIAAITSCTNTSNPRN++AAGL Sbjct: 361 TLAGPSNPHALLPTAELAKRGISGNVQSDEGRMPDGAVIIAAITSCTNTSNPRNMVAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 +ARNANA GL RKPWVKTSLAPGSK V++YLEEANLL ELESLGFG+V FACTTCNGMSG Sbjct: 421 IARNANALGLMRKPWVKTSLAPGSKTVKMYLEEANLLSELESLGFGVVAFACTTCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDP IQQE++DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE Sbjct: 481 ALDPAIQQEIVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KD LG D G PV L +IWPSD EIDA++ +VKPEQFR Y PMFD V PLY Sbjct: 541 KDALGYDDKGNPVTLKDIWPSDEEIDAIVKRAVKPEQFRATYIPMFDADATSRTYVDPLY 600 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 +WRPQSTYIRRPPYWEGALAGER+LKGMRPLAVL DNITTDHLSPSNAIM DSAAGEYL Sbjct: 601 EWRPQSTYIRRPPYWEGALAGERSLKGMRPLAVLPDNITTDHLSPSNAIMADSAAGEYLA 660 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724 KMG+PEEDFNSYATHRGDHLTAQRATFANPKL NEMA+V+G+V GSLARIEPEG V RM Sbjct: 661 KMGVPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVNGEVVHGSLARIEPEGQVVRM 720 Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784 WEAIETYM RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNL+GMG Sbjct: 721 WEAIETYMQRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMG 780 Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844 VLPLEF +G R T GIDGTE FDVIG APRA + ++I NGE +E PV CRLDT EE Sbjct: 781 VLPLEFPSGTTRKTLGIDGTETFDVIGEFAPRATMRLVIRLANGEGIETPVICRLDTQEE 840 Query: 845 VSIYEAGGVLQRFAQDFLESN 865 VS ++AGGVLQRFAQDFLE++ Sbjct: 841 VSTFQAGGVLQRFAQDFLEAS 861 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: 2224 Number of extensions: 83 Number of successful extensions: 1 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: 866 Length adjustment: 42 Effective length of query: 825 Effective length of database: 824 Effective search space: 679800 Effective search space used: 679800 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 24 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