Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate RR42_RS14490 RR42_RS14490 aconitate hydratase
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Cup4G11:RR42_RS14490 Length = 901 Score = 667 bits (1721), Expect = 0.0 Identities = 363/861 (42%), Positives = 521/861 (60%), Gaps = 44/861 (5%) Query: 34 AYAKLPYTSRVLAENLVRRCEPEMLT-------ASLKQIIESKQELDFPWFPARVVCHDI 86 A +LP + RV+ E+++R C+ + +T A K + E E+ P+ ARVV D Sbjct: 35 AVERLPVSIRVVLESVLRNCDGKKVTEEHVRQLAHWKPVAERVDEI--PFVVARVVLQDF 92 Query: 87 LGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIED 146 G L DLA +R+ G +P ++ P+VP L+VDHS+ +++ +K+A N +E Sbjct: 93 TGVPLLADLAAMRNVAEKMGKNPKKIEPLVPVDLVVDHSVQIDHFR-EKNALDLNMKLEF 151 Query: 147 RRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSH 206 +RN +R+ F+ W +AF V+ G GI+HQ+NLE ++ +H ++GV +PDTLVGTDSH Sbjct: 152 QRNNERYQFMKWGMQAFDTFGVVQPGFGIVHQVNLEYLARGVHKKDGVYYPDTLVGTDSH 211 Query: 207 TPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEF 266 T ++ +GV+ GVGG+EAE+ MLG+ Y PD++GVEL G+ + G+TATD+VL +TE Sbjct: 212 TTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVELKGRLREGVTATDLVLTITEM 271 Query: 267 LRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREA 326 LR +KVV ++EFFGEG +L L DRATI NM PE+GAT F +D++T+DY TGR Sbjct: 272 LRREKVVGKFVEFFGEGTASLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTE 331 Query: 327 EQVKLVETYAKTAGLWS-DDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV--------- 376 E++ E Y + ++ + Y + DL +V ++AGP P R+ Sbjct: 332 EEIAAFEGYFRAQKMFGVPKAGEIDYTNVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTF 391 Query: 377 ------PTSELAARGISGEVEN-----EPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLL 425 PT+E E++ + + G V+IAAITSCTNTSNP ++AAGLL Sbjct: 392 ASLFAKPTAENGFNKDIAELDKTYTTADGVNVKSGDVLIAAITSCTNTSNPSVLLAAGLL 451 Query: 426 ARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGA 485 A+ A GL P +KTSLAPGS+ V YL+ A LLP LE LGFG+ + CTTC G +G Sbjct: 452 AKKAVEAGLKVAPHIKTSLAPGSRVVTEYLQAAGLLPYLEKLGFGVTAYGCTTCIGNAGD 511 Query: 486 LDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEK 545 L P + + + DL A AVLSGNRNF+ RIHP + FLASPPLVVAYAIAG + D+ Sbjct: 512 LTPELNEAITRNDLVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNVTRDLMT 571 Query: 546 DVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPM---FDLSVDYGDKVSP 602 + +G K G+ + L +IWP+ EI A++ ++ + F+ YE + L Sbjct: 572 EPVGTGKGGREIYLGDIWPTSEEIHALMKYAMDSKVFKINYEQVKKPSKLWAKVKGTKGQ 631 Query: 603 LYDWRPQSTYIRRPPYWEG----ALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSA 658 +YDW P+STYI PP+++G A + +++ R L V GD++TTDH+SP+ +I S Sbjct: 632 VYDW-PKSTYIAEPPFFDGFGMEPAATQSSVRNARALGVFGDSVTTDHISPAGSIKESSP 690 Query: 659 AGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIV--DGKVKQGSLARIE 716 AG+YL G+ + DFNSY + RG+H R TFAN ++KN M V DG +G + + Sbjct: 691 AGKYLLANGVLKADFNSYGSRRGNHEVMMRGTFANVRIKNLMLPVKADGSRVEGGVTLHQ 750 Query: 717 PEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIH 776 P G +++A Y+ P ++ G +YG GSSRDWAAKG +L GV+A++ FERIH Sbjct: 751 PSGEALSIYDAAMKYIAEGTPTVVFGGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIH 810 Query: 777 RTNLVGMGVLPLEFKAGENRATYGIDGTEVFD---VIGSIAPRADLTVIITRKNGERVEV 833 R+NLVGMGVLPL+FK ++ T GI G E FD + G + P+ D+T++I R NG+ V Sbjct: 811 RSNLVGMGVLPLQFKGSDSVQTLGIVGDETFDIEGIEGELKPQQDVTLVIKRANGDVQRV 870 Query: 834 PVTCRLDTAEEVSIYEAGGVL 854 P+ R+DT EV Y GG+L Sbjct: 871 PLLLRIDTPIEVDYYNHGGIL 891 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: 2000 Number of extensions: 103 Number of successful extensions: 10 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: 901 Length adjustment: 43 Effective length of query: 824 Effective length of database: 858 Effective search space: 706992 Effective search space used: 706992 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