Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate BPHYT_RS30145 BPHYT_RS30145 aconitate hydratase
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__BFirm:BPHYT_RS30145 Length = 865 Score = 1467 bits (3797), Expect = 0.0 Identities = 727/863 (84%), Positives = 785/863 (90%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT RK LPGT LD+FDTR A++AI PGAY KLPYTSRVLAENLVRRC+P LTASLKQ Sbjct: 1 MNTANRKRLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPVTLTASLKQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 IIE K+ELDFPWFPARVVCHDILGQTALVDLAGLRDAIAA+GGDPA VNPVVPTQL+VDH Sbjct: 61 IIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPALVNPVVPTQLVVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE GGFD DAFAKNRAIEDRRNEDRF FINWT++AF+N+DVIP GNGI+HQINLERM Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKRAFRNVDVIPPGNGILHQINLERM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPV+ ++GVAFPDTLVGTDSHTP VDALGVIAIGVGGLEAESVMLGRASYMRLPDI+GV Sbjct: 181 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASYMRLPDIVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 ELTGKP GITATD+VL+LTEFLR +KVV +YLEF+G G LTLGDRATI+NM PEFGA Sbjct: 241 ELTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFYGTGTAKLTLGDRATIANMAPEFGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TAAMF ID+QT+ YL LTGR+ E VK VETYAK GLW+D L A Y R L FDLS+VVR Sbjct: 301 TAAMFSIDEQTIKYLKLTGRDDELVKRVETYAKKTGLWADSLVNAEYERVLKFDLSTVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424 T+AGPSNPH R+P SELAARGISG+VENEPGLMPDGAVIIAAITSCTNT+NPRN+IAAGL Sbjct: 361 TLAGPSNPHRRLPVSELAARGISGKVENEPGLMPDGAVIIAAITSCTNTNNPRNMIAAGL 420 Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484 LARNAN +GLTRKPW KTSLAPGSKAV LYLEEA LLPELE LGFG+V +ACT+CNGMSG Sbjct: 421 LARNANRRGLTRKPWAKTSLAPGSKAVTLYLEEAGLLPELEQLGFGVVAYACTSCNGMSG 480 Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544 ALDPVIQ+E+++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE Sbjct: 481 ALDPVIQKEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540 Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604 KDVLG+D DG+ V L +IWP+DAEIDA++A+SVKPEQFRKVYEPMF +SVD G+K PLY Sbjct: 541 KDVLGIDADGQAVTLKDIWPTDAEIDAIVASSVKPEQFRKVYEPMFAVSVDTGEKADPLY 600 Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664 +WRP STYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAI+ DSA+GEYL Sbjct: 601 NWRPMSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILADSASGEYLA 660 Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724 KMGLPEEDFNSYATHRGDHLTAQRATFANP LKNEM + DGKVK GSLARIEPEG VTRM Sbjct: 661 KMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVLEDGKVKAGSLARIEPEGKVTRM 720 Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784 WEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAG EAIVAEGFERIHRTNLVGMG Sbjct: 721 WEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTNLVGMG 780 Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844 VLPLEFK G NR T IDGTE FDVIG PRADLT++I RKNGERVEVPVTCRLDTAEE Sbjct: 781 VLPLEFKPGVNRLTLAIDGTETFDVIGERKPRADLTLVIHRKNGERVEVPVTCRLDTAEE 840 Query: 845 VSIYEAGGVLQRFAQDFLESNLK 867 VSIYEAGGVLQRFAQDFLES+ K Sbjct: 841 VSIYEAGGVLQRFAQDFLESSKK 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: 2271 Number of extensions: 93 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