Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 7026694 Shewana3_3827 aconitate hydratase (RefSeq)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__ANA3:7026694 Length = 863 Score = 1668 bits (4319), Expect = 0.0 Identities = 836/863 (96%), Positives = 847/863 (98%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT YRKPLPGTALDYFDTREA+EAI+PGAYAKLPYTSRVLAENLVRRCEPE LTASLKQ Sbjct: 1 MNTLYRKPLPGTALDYFDTREAVEAISPGAYAKLPYTSRVLAENLVRRCEPEALTASLKQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH Sbjct: 61 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM Sbjct: 121 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPV+HAR+GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV Sbjct: 181 SPVVHARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGKPQPGITATDIVLALTEFLR +KVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA Sbjct: 241 ELTGKPQPGITATDIVLALTEFLRKEKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMFYIDQQTLDYLTLTGR EQVKLVETYAKT GLWSDDLK A YPRTLHFDLSSVVR Sbjct: 301 TAAMFYIDQQTLDYLTLTGRSDEQVKLVETYAKTTGLWSDDLKHAEYPRTLHFDLSSVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 TIAGPSNPHARVPT+ELAARGISG VENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL Sbjct: 361 TIAGPSNPHARVPTTELAARGISGVVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 LARNANAKGL+RKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG Sbjct: 421 LARNANAKGLSRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE Sbjct: 481 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KDVLG DKDG PVRLI+IWPSDAEIDAVIA SVKPEQFR+VYEPMFDLSVDYGDKV+PLY Sbjct: 541 KDVLGHDKDGNPVRLIDIWPSDAEIDAVIAKSVKPEQFRRVYEPMFDLSVDYGDKVTPLY 600 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH Sbjct: 601 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 660 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMA+VDGKVKQGSLARIEPEG VTRM Sbjct: 661 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAVVDGKVKQGSLARIEPEGQVTRM 720 Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG Sbjct: 721 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 780 Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844 VLPLEFKAGENRATYGIDGTEVFDV G IAPRADLTVIITRKNGERVEVPVTCRLDTAEE Sbjct: 781 VLPLEFKAGENRATYGIDGTEVFDVYGDIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 840 Query: 845 VSIYEAGGVLQRFAQDFLESNLK 867 VSIY AGGVLQRFAQDFLESNLK Sbjct: 841 VSIYSAGGVLQRFAQDFLESNLK 863 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: 2433 Number of extensions: 94 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: 863 Length adjustment: 42 Effective length of query: 825 Effective length of database: 821 Effective search space: 677325 Effective search space used: 677325 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