Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_043771237.1 U743_RS05220 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000733765.1:WP_043771237.1 Length = 865 Score = 1400 bits (3623), Expect = 0.0 Identities = 693/860 (80%), Positives = 763/860 (88%), Gaps = 1/860 (0%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT+YRKPLPGT LDYFD R A++AI PGAY LPYTSRVLAENLVRRC+P MLT +LKQ Sbjct: 1 MNTEYRKPLPGTELDYFDVRAAVDAIQPGAYDGLPYTSRVLAENLVRRCDPAMLTDALKQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 +IE +++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVPTQLIVDH Sbjct: 61 LIERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAERGGDPAKVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE+ GF++DAF KNRAIEDRRNEDRFHFI+WT++AF+NIDV+P GNGIMHQINLERM Sbjct: 121 SLAVEHAGFEEDAFEKNRAIEDRRNEDRFHFIDWTKQAFENIDVVPPGNGIMHQINLERM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPV+HA +GVA+PDTLVGTDSHTPHVDALGVIA+GVGGLEAESVMLGRASYMRLPDIIGV Sbjct: 181 SPVVHAVDGVAYPDTLVGTDSHTPHVDALGVIAVGVGGLEAESVMLGRASYMRLPDIIGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGKP PG+T+TDIVLALTEFLR +KVVS+YLEFFGEGA AL+LGDRATISNMTPE+GA Sbjct: 241 ELTGKPAPGMTSTDIVLALTEFLRNEKVVSAYLEFFGEGASALSLGDRATISNMTPEYGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMFYID+QT+DYL LTGR EQV LVE YA+ GLW+DDLK A Y R L FDLSSV R Sbjct: 301 TAAMFYIDEQTIDYLKLTGRTPEQVDLVERYARHTGLWADDLKTAEYERVLRFDLSSVTR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVE-NEPGLMPDGAVIIAAITSCTNTSNPRNVIAAG 423 +AGPS PHARV T++LA GISG+VE E G MPDGAVIIAAITSCTNTSNPRNVIAAG Sbjct: 361 NLAGPSRPHARVSTADLAKAGISGKVELPEDGSMPDGAVIIAAITSCTNTSNPRNVIAAG 420 Query: 424 LLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMS 483 LLARNAN +GLTRKPWVK+S APGSKAV+LY+EE L EL LGFGIV FACTTCNGMS Sbjct: 421 LLARNANQRGLTRKPWVKSSFAPGSKAVKLYMEECGLQDELNRLGFGIVAFACTTCNGMS 480 Query: 484 GALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDI 543 GALDP IQQE+IDRDLY+ AVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT RFDI Sbjct: 481 GALDPKIQQEIIDRDLYSVAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTTRFDI 540 Query: 544 EKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPL 603 EKDVLG DKDG V L ++WPSD EIDA +A++VKPE FR VY+PMF + DK+SPL Sbjct: 541 EKDVLGYDKDGNAVTLKDLWPSDEEIDATVASAVKPEHFRSVYDPMFSFKILDDDKISPL 600 Query: 604 YDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYL 663 YDWR QSTYIRRPPYWEGALA +LKGMR LAVLGDNITTDHLSPSNAIM DSAAGEYL Sbjct: 601 YDWRAQSTYIRRPPYWEGALATAPSLKGMRALAVLGDNITTDHLSPSNAIMADSAAGEYL 660 Query: 664 HKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTR 723 KMGLPEEDFNSYATHRGDHLTAQRAT ANPKL NEMA+VDG+VKQGSL R+EP+G V R Sbjct: 661 AKMGLPEEDFNSYATHRGDHLTAQRATLANPKLINEMAVVDGEVKQGSLTRLEPDGKVVR 720 Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783 MWEAIE Y +RKQ LI+IAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM Sbjct: 721 MWEAIEAYQERKQALIVIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 780 Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843 GV+PL+F+ G R T GIDG+E FDV+G+ +P A LT+ I R+ GE +EVPV CRLDT E Sbjct: 781 GVMPLQFQEGTTRKTMGIDGSETFDVVGTPSPGATLTLHIHRREGETLEVPVICRLDTQE 840 Query: 844 EVSIYEAGGVLQRFAQDFLE 863 E+ IYEAGGVLQRFAQDFLE Sbjct: 841 ELRIYEAGGVLQRFAQDFLE 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: 2201 Number of extensions: 93 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: 865 Length adjustment: 42 Effective length of query: 825 Effective length of database: 823 Effective search space: 678975 Effective search space used: 678975 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