Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__BFirm:BPHYT_RS33980 Length = 905 Score = 646 bits (1666), Expect = 0.0 Identities = 352/861 (40%), Positives = 520/861 (60%), Gaps = 45/861 (5%) Query: 37 KLPYTSRVLAENLVRRCEPEMLTAS-LKQIIESKQEL----DFPWFPARVVCHDILGQTA 91 +LP + R++ E+++R + + + ++Q+ K + P+ +RVV D G Sbjct: 37 RLPVSIRIVLESVLRNYDGKKIAEEHIEQLANWKPTAARVDEIPFVVSRVVLQDFTGVPL 96 Query: 92 LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151 L D+A +R G DP + P+VP L+VDHS+ +++ +K+A N +E +RN + Sbjct: 97 LADIAAMRGVAKHMGKDPKSIEPLVPVDLVVDHSVQIDHFR-EKNALDLNMKLEFQRNNE 155 Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR----NGVAFPDTLVGTDSHT 207 R+ F+ W +AF V+P G GI+HQ+NLE ++ +H + + V +PD+LVGTDSHT Sbjct: 156 RYQFMKWGMQAFDTFKVVPPGVGIVHQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHT 215 Query: 208 PHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFL 267 ++ +GV+ GVGG+EAE+ MLG+ Y PD++GVEL GK + G+TATD+VL +TE L Sbjct: 216 TMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVELKGKLREGLTATDLVLTVTELL 275 Query: 268 RAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAE 327 R +KVV ++EFFGEG ++L+L DRATI NM PE+GAT F +D++T++Y TGR Sbjct: 276 RKEKVVGKFVEFFGEGTKSLSLPDRATIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDA 335 Query: 328 QVKLVETYAKTAGLWS-DDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV---------- 376 ++ E Y K GL+ Q Y + + DL +V ++AGP P R+ Sbjct: 336 EISAFENYFKAQGLFGIPKAGQIDYTKVVTLDLGTVTPSLAGPKRPQDRIEIGHVKSTFS 395 Query: 377 -----PTSELA----ARGISGEVENEPGL-MPDGAVIIAAITSCTNTSNPRNVIAAGLLA 426 P +E A + + G+ + +G ++IAAITSCTNTSNP ++AAGLLA Sbjct: 396 DLFSKPVAENGFAKKAADLEAQYTTSNGVDVKNGDILIAAITSCTNTSNPSVLLAAGLLA 455 Query: 427 RNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGAL 486 + A GLT P +KTSLAPGS+ V YL + +L+ L+ LGF + + CTTC G +G L Sbjct: 456 KKAVEAGLTVAPHIKTSLAPGSRIVTEYLTKTDLMKYLDKLGFTLAAYGCTTCIGNAGDL 515 Query: 487 DPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKD 546 P + + + D+ A AVLSGNRNF+ RIHP + FLASPPLVVAYAIAG I D+ + Sbjct: 516 TPELNEAITKNDIVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNITRDLMTE 575 Query: 547 VLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF---DLSVDYGDKVSPL 603 +G K GK + L +IWP+ E++ ++ ++ + FRK Y + DL + + Sbjct: 576 PVGKGKGGKDIYLGDIWPTSEEVNELLKFALDADAFRKNYSALTKKGDLWSKIEGEEGQV 635 Query: 604 YDWRPQSTYIRRPPYWEGALAGE-----RTLKGMRPLAVLGDNITTDHLSPSNAIMMDSA 658 YDW P+STYI PP++ + + +K R L + GD++TTDH+SP+ +I DS Sbjct: 636 YDW-PKSTYIAEPPFFGKDFSMQPADSIAAVKDARALGIFGDSVTTDHISPAGSIKEDSP 694 Query: 659 AGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQGSLARIE 716 AG++L + G+ + DFNSY + RG+H R TFAN ++KN M A DG +G L + Sbjct: 695 AGKWLKENGVQKADFNSYGSRRGNHDVMMRGTFANVRIKNLMIPAKADGTRVEGGLTIHQ 754 Query: 717 PEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIH 776 P G +++A Y+D P ++ AG +YG GSSRDWAAKG +L GV+ +VA FERIH Sbjct: 755 PSGEQLSIYDAAMKYIDAGTPTVVFAGEEYGTGSSRDWAAKGTQLLGVKVVVARSFERIH 814 Query: 777 RTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLTVIITRKNGERVEV 833 R+NLVGMGVLPL+FK ++ + GI G E +D+ G P+ ++T++I K G+ V Sbjct: 815 RSNLVGMGVLPLQFKGSDSVQSLGITGEETYDIEGLGADFKPQQEVTLVIRDKEGKEKRV 874 Query: 834 PVTCRLDTAEEVSIYEAGGVL 854 V R+DT EV Y+ GG+L Sbjct: 875 QVLLRIDTPIEVDYYKHGGIL 895 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: 1919 Number of extensions: 105 Number of successful extensions: 9 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: 905 Length adjustment: 43 Effective length of query: 824 Effective length of database: 862 Effective search space: 710288 Effective search space used: 710288 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