Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_086511660.1 BZY95_RS20065 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_002151265.1:WP_086511660.1 Length = 869 Score = 1364 bits (3530), Expect = 0.0 Identities = 683/866 (78%), Positives = 749/866 (86%), Gaps = 7/866 (0%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNTQYRKPLPGT LDYFD REA+E I PGAY LPYTSRVLAE LVRRCEPE+LT +LKQ Sbjct: 1 MNTQYRKPLPGTELDYFDVREAVEEIQPGAYDTLPYTSRVLAEQLVRRCEPELLTDALKQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 +IE +++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDP++VNPVVPTQLIVDH Sbjct: 61 LIERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE GG D DAFAKNRAIEDRRNEDRFHFI+WT+ AFKN+DVIP GNGIMHQINLE+M Sbjct: 121 SLAVECGGDDPDAFAKNRAIEDRRNEDRFHFIDWTRTAFKNVDVIPAGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPVI AR+GVA+PDT VGTDSHTPH+D LGVIAIGVGGLEAE+VMLGR S MRLPDI+GV Sbjct: 181 SPVIQARDGVAYPDTCVGTDSHTPHIDCLGVIAIGVGGLEAETVMLGRPSMMRLPDIVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGK Q GITATDIVLA+TEFLR ++VV +YLEFFGEGA++LT+GDRATISNMTPE+GA Sbjct: 241 ELTGKRQSGITATDIVLAITEFLRQERVVGAYLEFFGEGADSLTIGDRATISNMTPEYGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMFYIDQQTLDYL +TGRE EQV LVE YAKT GLW+D LK Y R L FDLS+V R Sbjct: 301 TAAMFYIDQQTLDYLAITGREPEQVALVENYAKTVGLWADSLKNVQYERVLTFDLSTVER 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEV-----ENEPGLMPDGAVIIAAITSCTNTSNPRNV 419 +AGPSNPH R+PTS LA RGI+ + E + G MPDGAVIIAAITSCTNTSNPRNV Sbjct: 361 NLAGPSNPHRRLPTSALAERGIAVNLELALAEEKAGRMPDGAVIIAAITSCTNTSNPRNV 420 Query: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479 +AAGLLA+ AN GL RKPWVK+S APGSK +LYLEEA LLPELE LGFGIV +ACTTC Sbjct: 421 VAAGLLAKKANELGLVRKPWVKSSFAPGSKVARLYLEEAGLLPELEKLGFGIVAYACTTC 480 Query: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539 NGMSGAL P IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+ Sbjct: 481 NGMSGALRPEIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 540 Query: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599 RFDIEKD LG DK G PV L ++WPSD EIDA++ VKPEQF++VY PMF+L + Sbjct: 541 RFDIEKDALGYDKAGNPVTLKDLWPSDEEIDAIVGEYVKPEQFKQVYIPMFNLD-EVEQA 599 Query: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659 SPLYDWRPQSTYIRRPPYWEG +A ER LKGMRPLA+L DNITTDHLSPSNAI++DSAA Sbjct: 600 KSPLYDWRPQSTYIRRPPYWEGNMARERGLKGMRPLAILPDNITTDHLSPSNAILLDSAA 659 Query: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVD-GKVKQGSLARIEPE 718 GEYL KMGLPEEDFNSYATHRGDHLTAQRAT ANPKL NEM + G+V QGSLARIEPE Sbjct: 660 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATLANPKLFNEMVRDEKGEVIQGSLARIEPE 719 Query: 719 GIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 778 G VTRMWEAIETYM+R QPLI+IAGADYGQGSSRDWAAKGV LAGVEAIVAEGFERIHRT Sbjct: 720 GKVTRMWEAIETYMERGQPLIVIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRT 779 Query: 779 NLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCR 838 NLVGMGV+PL+F+ G R T +DGTE +DV G AP A LT++I R G VPV CR Sbjct: 780 NLVGMGVMPLQFQEGTTRHTLKLDGTETYDVEGKPAPGATLTLVIHRAGGNSERVPVLCR 839 Query: 839 LDTAEEVSIYEAGGVLQRFAQDFLES 864 LDTAEEVS+Y AGGVLQRFAQDFLES Sbjct: 840 LDTAEEVSVYSAGGVLQRFAQDFLES 865 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: 2180 Number of extensions: 88 Number of successful extensions: 5 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: 869 Length adjustment: 42 Effective length of query: 825 Effective length of database: 827 Effective search space: 682275 Effective search space used: 682275 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