Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 5209348 Shew_1822 aconitate hydratase (RefSeq)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__PV4:5209348 Length = 862 Score = 1477 bits (3824), Expect = 0.0 Identities = 728/861 (84%), Positives = 791/861 (91%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MN+ +RKPLPG+ALDYFDTR A+EA++ GAY KLPYT++VLAENLVRRCEPE+L +L Q Sbjct: 1 MNSLHRKPLPGSALDYFDTRAAVEALSAGAYDKLPYTAKVLAENLVRRCEPELLNDALSQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 +I+ K++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDP++VNPVVPTQLIVDH Sbjct: 61 LIDRKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE+ GF+KDAF KNRAIEDRRNEDRFHFINWT+ AFKN+DVI GNGIMHQINLE+M Sbjct: 121 SLAVEHAGFEKDAFEKNRAIEDRRNEDRFHFINWTKTAFKNVDVIQPGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPVI AR+GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGR SYMRLPDI+GV Sbjct: 181 SPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRPSYMRLPDIVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGK Q GITATDIVLALTEFLR +KVVS+YLEFFGEGA LTLGDRATISNMTPEFGA Sbjct: 241 ELTGKRQSGITATDIVLALTEFLRQEKVVSAYLEFFGEGAADLTLGDRATISNMTPEFGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 +A MFYIDQQT+DYLT+TGR++EQVKLVE YAKT GLW+D LK A Y R L FDLSSVVR Sbjct: 301 SAGMFYIDQQTIDYLTITGRDSEQVKLVENYAKTTGLWADSLKDAEYERVLTFDLSSVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 IAGPSNPH RV TSELA++GI+G VE + LMPDGAVIIAAITSCTNTSNPRNVIAAGL Sbjct: 361 NIAGPSNPHRRVATSELASQGIAGVVEQDDKLMPDGAVIIAAITSCTNTSNPRNVIAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 LA+ AN GL RKPWVKTS APGSK +LYL++A LLPELE LGFGIVGFACTTCNGMSG Sbjct: 421 LAKKANELGLVRKPWVKTSFAPGSKVAELYLKDAGLLPELEQLGFGIVGFACTTCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE Sbjct: 481 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KD+LG D G+P+RL +IWPSD EIDA++ ASVKP+QFR +Y PMFDL+VDYG+ V+PLY Sbjct: 541 KDILGHDDKGEPIRLKDIWPSDEEIDAIVKASVKPQQFRDIYTPMFDLAVDYGEDVNPLY 600 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAI+ SAAGEYL Sbjct: 601 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLA 660 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724 KMGLPE DFNSYATHRGDHLTAQRATFANPKL NEMA+VDG+VKQGSL R+EPEG V RM Sbjct: 661 KMGLPEVDFNSYATHRGDHLTAQRATFANPKLINEMALVDGEVKQGSLTRLEPEGEVMRM 720 Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG Sbjct: 721 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 780 Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844 VLPLEFKAGENR TYGIDG+E FDVIG PRADLTV+ITR+NGERVEVPV CRLDTA+E Sbjct: 781 VLPLEFKAGENRHTYGIDGSETFDVIGEPTPRADLTVVITRQNGERVEVPVICRLDTADE 840 Query: 845 VSIYEAGGVLQRFAQDFLESN 865 V +Y+AGGVLQRFAQDFLE+N Sbjct: 841 VLVYQAGGVLQRFAQDFLEAN 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: 2250 Number of extensions: 104 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: 862 Length adjustment: 42 Effective length of query: 825 Effective length of database: 820 Effective search space: 676500 Effective search space used: 676500 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 17 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