Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate RR42_RS11270 RR42_RS11270 aconitate hydratase
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Cup4G11:RR42_RS11270 Length = 865 Score = 1496 bits (3874), Expect = 0.0 Identities = 744/861 (86%), Positives = 789/861 (91%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT RKPLPGT LD+FDTR A++AI PGAY KLPYTSRVLAENLVRRC+P LT SLKQ Sbjct: 1 MNTANRKPLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLKQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 IIE KQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAA+GGDP VNPVVPTQL+VDH Sbjct: 61 IIERKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPVMVNPVVPTQLVVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE GGFD DAFAKNRAIEDRRNEDRF FINWT+KAFKN+DVIP GNGI+HQINLERM Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKKAFKNVDVIPPGNGILHQINLERM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPV+ ++GVAFPDTLVGTDSHTP VDALGVIAIGVGGLEAESVMLGRAS+MRLPDIIGV Sbjct: 181 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASWMRLPDIIGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGKPQPGITATD VLALTEFLR +KVVSSYLEFFGEG LTLGDRATISNM PEFG+ Sbjct: 241 ELTGKPQPGITATDTVLALTEFLRKEKVVSSYLEFFGEGTTHLTLGDRATISNMAPEFGS 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMFYID+QT+ YL LTGR+ VKLVETYAK AGLW+D LK A YPR L FDLS+VVR Sbjct: 301 TAAMFYIDEQTIKYLKLTGRDDALVKLVETYAKEAGLWADSLKNAEYPRVLRFDLSTVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 IAGPSNPH RVPTSELAARGISG+VENEPGLMPDGAVIIAA+TSCTNT+NPRN++AAGL Sbjct: 361 NIAGPSNPHKRVPTSELAARGISGKVENEPGLMPDGAVIIAAVTSCTNTNNPRNMVAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 LARNAN GLTRKPWVK+SLAPGSKAV LYLEEANLLPELE LGFG+V +ACT+CNGMSG Sbjct: 421 LARNANKLGLTRKPWVKSSLAPGSKAVTLYLEEANLLPELEQLGFGVVAYACTSCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDPVIQ+EV+DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE Sbjct: 481 ALDPVIQKEVVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KDVLG D DGKPV L +IWPSD EIDAV+AASVKP QFRKVYEPMF ++ D G+K SPLY Sbjct: 541 KDVLGTDADGKPVTLKDIWPSDEEIDAVVAASVKPAQFRKVYEPMFAVTADTGEKASPLY 600 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 DWR STYIRRPPYWEGALAGER L GMRPLAVLGDNITTDHLSPSNAIM+DSAAGEYL Sbjct: 601 DWREMSTYIRRPPYWEGALAGERALTGMRPLAVLGDNITTDHLSPSNAIMLDSAAGEYLA 660 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724 KMGLPEEDFNSYATHRGDHLTAQRATFANP LKNEM +VDGKVK GSLARIEPEG VTRM Sbjct: 661 KMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVVVDGKVKPGSLARIEPEGKVTRM 720 Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784 WEAIETYM RKQPLI++AGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG Sbjct: 721 WEAIETYMARKQPLIVVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 780 Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844 VLPLEFK G NRAT GIDGTE +DVIG PR DLT+++ RKNGERVEVPVTCRLDTAEE Sbjct: 781 VLPLEFKPGVNRATLGIDGTETYDVIGDRTPRCDLTLVMHRKNGERVEVPVTCRLDTAEE 840 Query: 845 VSIYEAGGVLQRFAQDFLESN 865 VSIYEAGGVLQRFAQDFLES+ Sbjct: 841 VSIYEAGGVLQRFAQDFLESS 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: 2331 Number of extensions: 91 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: 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 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