Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF4113 PS417_21070 aconitate hydratase
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__WCS417:GFF4113 Length = 864 Score = 1444 bits (3738), Expect = 0.0 Identities = 723/860 (84%), Positives = 775/860 (90%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT++RKPLPG+ LDYFD R A++AI+PGAYA LPYTSRVLAENLVRRC+P L ASL Q Sbjct: 1 MNTEFRKPLPGSRLDYFDARAAVDAISPGAYATLPYTSRVLAENLVRRCDPATLNASLSQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 +IE K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPAQVNPVVPTQLIVDH Sbjct: 61 LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE GGFD DAF KNRAIEDRRNEDRFHFI WT+KAFKN+DVIP GNGIMHQINLE+M Sbjct: 121 SLAVEAGGFDPDAFEKNRAIEDRRNEDRFHFIEWTKKAFKNVDVIPPGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPVI R+GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS+MRLP+ +GV Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGK PGITATD+VLALTEFLR QKVV ++LEFFGEGA ALTLGDRATISNM PE+GA Sbjct: 241 ELTGKLLPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMFYIDQQT+ YL LTGRE EQV LVE YA+ GLW+DDLK A Y R L FDLSSVVR Sbjct: 301 TAAMFYIDQQTIAYLKLTGREDEQVTLVEQYARHTGLWADDLKGAQYERGLTFDLSSVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 +AGPSNPHARV TS+LA++GISG+ + PG MPDGAVIIAAITSCTNTSNPRNVIAAGL Sbjct: 361 NMAGPSNPHARVATSDLASKGISGQWDEVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 LARNAN GLTRKPWVK+SLAPGSK V +YLEEA L ELE LGFG+V FACTTCNGMSG Sbjct: 421 LARNANKLGLTRKPWVKSSLAPGSKTVAMYLEEAGLGHELEKLGFGVVAFACTTCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE Sbjct: 481 ALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KDVLGLD +GK +RL +IWPSD EIDAV+ ASVKPEQFR VY PMF + D G KV+PLY Sbjct: 541 KDVLGLDANGKEIRLQDIWPSDEEIDAVVKASVKPEQFRAVYIPMFAIHEDTGPKVAPLY 600 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 DWRPQSTYIRRPPYWEGALAG R LKGMRPLAVL DNITTDHLSPSNAIM+DSAAGEYL Sbjct: 601 DWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 660 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724 KMGLPE DFNSYATHRGDHLTAQRATFANPKL NEM + +GKVKQGSLARIEPEG VTRM Sbjct: 661 KMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVVENGKVKQGSLARIEPEGQVTRM 720 Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784 WEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI AEGFERIHRTNLVGMG Sbjct: 721 WEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMG 780 Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844 VLPLEF G +R T IDG+E +DV+G+ PRA LT++I RKNGERVEVPVTCRLDTAEE Sbjct: 781 VLPLEFLPGTDRHTLKIDGSETYDVVGARTPRAQLTLVINRKNGERVEVPVTCRLDTAEE 840 Query: 845 VSIYEAGGVLQRFAQDFLES 864 VSIYEAGGVLQRFAQDFLES Sbjct: 841 VSIYEAGGVLQRFAQDFLES 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: 2222 Number of extensions: 92 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: 864 Length adjustment: 42 Effective length of query: 825 Effective length of database: 822 Effective search space: 678150 Effective search space used: 678150 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