Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_057508738.1 ABB28_RS11325 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_001431535.1:WP_057508738.1 Length = 871 Score = 1440 bits (3727), Expect = 0.0 Identities = 719/868 (82%), Positives = 775/868 (89%), Gaps = 7/868 (0%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MN YRK LPGTALDYFDTR A++AI PGAYA LPYTSRVLAENLVRRC+P L ASL+Q Sbjct: 1 MNESYRKNLPGTALDYFDTRAAVDAIQPGAYATLPYTSRVLAENLVRRCDPATLQASLRQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 +IE +Q+LDFPWFPARVVCHDILGQTALVDLAGLRDAIA GGDPAQ+NPVVPTQLIVDH Sbjct: 61 LIERRQDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADAGGDPAQINPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVEY GFDK AF +NRA+EDRRNEDRFHFINWT+KAFKN+DVIP GNGIMHQINLE+M Sbjct: 121 SLAVEYPGFDKAAFERNRAVEDRRNEDRFHFINWTRKAFKNVDVIPPGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPV+ R+GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS+MRLPDIIGV Sbjct: 181 SPVVQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPDIIGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTG+PQPGIT TDIVLALTEFLRA KVV +++EFFG GA AL++GDRATISNMTPEFGA Sbjct: 241 ELTGRPQPGITCTDIVLALTEFLRAAKVVGAWIEFFGAGASALSIGDRATISNMTPEFGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMF IDQQTLDYL LTGRE QV+LVETYAK AGLW+DDL Q Y R L FDLSSVVR Sbjct: 301 TAAMFSIDQQTLDYLRLTGREEPQVQLVETYAKAAGLWADDLAQVQYERVLQFDLSSVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGI-------SGEVENEPGLMPDGAVIIAAITSCTNTSNPR 417 +AGPSNPH RV TSELAARGI SG++E GLMPDGAVIIAAITSCTNTSNPR Sbjct: 361 NMAGPSNPHKRVATSELAARGIADEAKLASGKLEQAGGLMPDGAVIIAAITSCTNTSNPR 420 Query: 418 NVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACT 477 NVI A LLARNAN GLTRKPWVK+SLAPGSKAVQLYLEEA LL ELE LGFGIVGFACT Sbjct: 421 NVIGAALLARNANRAGLTRKPWVKSSLAPGSKAVQLYLEEAGLLGELEQLGFGIVGFACT 480 Query: 478 TCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 537 TCNGMSGALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASP LVVAYAIAG Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPALVVAYAIAG 540 Query: 538 TIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYG 597 T+RFDIEKD LG+D G + L ++WPSD EIDAV+ ASVKPEQFRKVY+PMF +V++G Sbjct: 541 TVRFDIEKDALGVDAQGNSITLKDLWPSDEEIDAVVKASVKPEQFRKVYDPMFTFTVEHG 600 Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657 +SPLY WRPQSTYIRRPPYWEGALAG RTL GMRPLAVLGDNITTDHLSPSNAI+ S Sbjct: 601 APISPLYAWRPQSTYIRRPPYWEGALAGARTLSGMRPLAVLGDNITTDHLSPSNAILASS 660 Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717 AAGEYL +MGLPEEDFNSYATHRGDHLTAQRATFANPKL NEMA+VDG VKQGSLAR+EP Sbjct: 661 AAGEYLAQMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGVVKQGSLARVEP 720 Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777 EG V RMWEAIETYM R+QPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI AEGFERIHR Sbjct: 721 EGQVLRMWEAIETYMLRRQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHR 780 Query: 778 TNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTC 837 TNL+GMGVLPLEFK G R T GIDGTE FDV G+ PRA+LT++I R++G ++ VPVTC Sbjct: 781 TNLIGMGVLPLEFKPGVTRLTLGIDGTETFDVTGARLPRAELTLVIHRRDGSQLMVPVTC 840 Query: 838 RLDTAEEVSIYEAGGVLQRFAQDFLESN 865 RLDTAEEVSIYEAGGVLQRFAQDFLE++ Sbjct: 841 RLDTAEEVSIYEAGGVLQRFAQDFLEAS 868 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: 2211 Number of extensions: 84 Number of successful extensions: 2 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: 871 Length adjustment: 42 Effective length of query: 825 Effective length of database: 829 Effective search space: 683925 Effective search space used: 683925 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