Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 6939202 Sama_3296 aconitate hydratase (RefSeq)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__SB2B:6939202 Length = 861 Score = 1427 bits (3693), Expect = 0.0 Identities = 707/862 (82%), Positives = 777/862 (90%), Gaps = 2/862 (0%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNTQ+RKPLPGT L +FDTREA++AIAPGA+ KLPYTS+VLAENL+R+ EP L L Q Sbjct: 1 MNTQFRKPLPGTNLSFFDTREAVDAIAPGAFDKLPYTSKVLAENLLRKAEPARLNDFLSQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 +I KQ+LDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPA+VNPVVPTQLIVDH Sbjct: 61 LIFRKQDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE+GGF+KDAF KNRAIEDRRN+DRFHFINWT+KAF+N+DVIP GNGIMHQINLE+M Sbjct: 121 SLAVEHGGFEKDAFEKNRAIEDRRNDDRFHFINWTKKAFRNVDVIPPGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPVI R+G+AFPDT VGTDSHTPHVD+LGVIAIGVGGLEAE+VMLGRAS+MRLPDI+GV Sbjct: 181 SPVIQVRDGIAFPDTCVGTDSHTPHVDSLGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGKP PGITATD+VLALTEFLR ++VV +YLEFFGEGA+ALTLGDRATISNMTPE+GA Sbjct: 241 ELTGKPNPGITATDVVLALTEFLRKERVVGAYLEFFGEGAKALTLGDRATISNMTPEYGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMFYID+QT+DYL LTGR+ +QV+LVE YAKT GLW+D + A Y R L FDLSSVVR Sbjct: 301 TAAMFYIDEQTIDYLRLTGRDEKQVELVENYAKTTGLWADAMTGADYGRILTFDLSSVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 +AGPSNPHAR+ TS+LAA+GI+ + + E G MPDGAVIIAAITSCTNTSNPRNVIAAGL Sbjct: 361 NMAGPSNPHARLATSDLAAKGIAADWQEESGKMPDGAVIIAAITSCTNTSNPRNVIAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 +ARNA KGL RKPWVKTSLAPGSKAV+LYL+EA LLP LE LGFGIV FACTTCNGMSG Sbjct: 421 IARNAVQKGLVRKPWVKTSLAPGSKAVELYLKEAGLLPYLEQLGFGIVAFACTTCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDPVIQQE+I+RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+RFDIE Sbjct: 481 ALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KDVLG+D G V L ++WP DAEIDA+I +SVKPEQFR VY+PMF+L+V+YG + PLY Sbjct: 541 KDVLGIDDAGNAVTLKDLWPEDAEIDAIIKSSVKPEQFRAVYDPMFNLAVEYGTE-KPLY 599 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 DWRPQSTYIRRPPYWEGALAGERTL GMRPLAVLGDNITTDHLSPSNAI+ SAAGEYL Sbjct: 600 DWRPQSTYIRRPPYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLA 659 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMA-IVDGKVKQGSLARIEPEGIVTR 723 KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM DGKVKQGSLAR+EPEG V R Sbjct: 660 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVKDADGKVKQGSLARLEPEGKVLR 719 Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783 MWE IETYM+RKQPLII+AG DYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTNLVGM Sbjct: 720 MWETIETYMERKQPLIIVAGKDYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLVGM 779 Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843 GVLPLEF GE R TYGIDGTE FDV G P A+LT++I R+NGE VEVPV CRLDTAE Sbjct: 780 GVLPLEFMPGETRMTYGIDGTETFDVKGERTPGAELTLLIRRQNGETVEVPVRCRLDTAE 839 Query: 844 EVSIYEAGGVLQRFAQDFLESN 865 EVSIYEAGGVLQRFAQDFL ++ Sbjct: 840 EVSIYEAGGVLQRFAQDFLANS 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: 2278 Number of extensions: 104 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: 861 Length adjustment: 42 Effective length of query: 825 Effective length of database: 819 Effective search space: 675675 Effective search space used: 675675 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 Apr 09 2024. 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