Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_043766717.1 U743_RS06915 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000733765.1:WP_043766717.1 Length = 883 Score = 727 bits (1876), Expect = 0.0 Identities = 391/851 (45%), Positives = 540/851 (63%), Gaps = 41/851 (4%) Query: 36 AKLPYTSRVLAENLVRRCEPEMLTASLKQIIESKQELDFP-----WFPARVVCHDILGQT 90 ++LP++ +VL ENL+R+ + E +T + S P + PARV+ D G Sbjct: 33 SRLPFSYKVLLENLLRKEDGESVTVEDIETFASADLRKLPAKEIAFTPARVLLQDFTGVP 92 Query: 91 ALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNE 150 +VDLA +RDA+ GGD ++NP+ P++L++DHS+ V++ G D+F N +E RN+ Sbjct: 93 CVVDLAAMRDAMTKLGGDAKKINPLCPSELVIDHSVMVDHYGA-ADSFDLNAKLEFNRNK 151 Query: 151 DRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPHV 210 +R+ F+ W Q A N V+P GI+HQ+N+E +S V+ +GV +PD+ GTDSHT V Sbjct: 152 ERYAFLRWGQNALDNFKVVPPDTGIVHQVNIEYLSRVVFDNDGVLYPDSCFGTDSHTTMV 211 Query: 211 DALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQ 270 + LGV+ GVGG+EAE+ MLG+ S M +P++IGV LTG G TATD+VL +TE LR + Sbjct: 212 NGLGVLGWGVGGIEAEAAMLGQPSTMLMPEVIGVRLTGALPEGATATDLVLTVTEMLRKR 271 Query: 271 KVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVK 330 VV ++EFFG+G LTL DRATI+NM PE+GAT +F ID++TL YL LTGR +QV+ Sbjct: 272 GVVEKFVEFFGDGLSELTLADRATIANMAPEYGATCGIFPIDEETLKYLRLTGRTEDQVE 331 Query: 331 LVETYAKTAGLWSDDLK-QAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSEL-------- 381 +V+ YA+ G+W + + +A Y LH +L S+ ++AGP P RV S++ Sbjct: 332 VVKAYAQAQGMWREKGEPEAEYSDVLHLELGSIQPSLAGPKRPQDRVLLSDVQANYQQAF 391 Query: 382 ----AARGISGEV----ENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKG 433 A R G +++ + DG V+IAAITSCTNTSNP +I AGLLARNA AKG Sbjct: 392 EADQAGRPTKGSAKVNYKDQDFQLDDGDVVIAAITSCTNTSNPAVLIGAGLLARNARAKG 451 Query: 434 LTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQE 493 +T KPWVKTSLAPGSK V YLE++ LL +LE+LGF +VG+ CTTC G SG L I + Sbjct: 452 ITVKPWVKTSLAPGSKVVTDYLEKSGLLEDLEALGFYVVGYGCTTCIGNSGPLPEPIAEA 511 Query: 494 VIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKD 553 V +L +VLSGNRNF+GR+H + +LASPPLVVAYA+AG++ D+ KD +G + D Sbjct: 512 VTANNLSVASVLSGNRNFEGRVHQDVRMNYLASPPLVVAYALAGSVDIDLNKDPIGENTD 571 Query: 554 GKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFD-------LSVDYGDKVSPLYDW 606 G+PV L +IWP EI +IA+S+ E F Y +FD L V GD+ Y+W Sbjct: 572 GQPVYLKDIWPKSQEIQDLIASSLNAEMFTTSYGKVFDGDDRWRGLDVPTGDR----YEW 627 Query: 607 RPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYL 663 R STY++ PPY+EG + G +K R LA+LGD++TTDH+SP+ AI DS AG+YL Sbjct: 628 RDDSTYVQNPPYFEGMTKEVPGLPAIKSARVLALLGDSVTTDHISPAGAIKQDSPAGKYL 687 Query: 664 HKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTR 723 + G+ DFNSY + RG+H R TFAN +++N+M V G +G + P G Sbjct: 688 MENGVKPADFNSYGSRRGNHEVMMRGTFANVRIRNKM--VPG--VEGGYTKHIPSGEQMA 743 Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783 +++A Y L++IAG +YG GSSRDWAAKG L G +A++AE FERIHR+NLVGM Sbjct: 744 IYDAAMKYQAEGTQLVVIAGKEYGTGSSRDWAAKGTNLLGAKAVIAESFERIHRSNLVGM 803 Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843 GV+PL FK G+N G+DG+E D+ G ++TV + NGE V R+DT + Sbjct: 804 GVVPLTFKDGQNAENLGLDGSEQIDIEGLEQGAKEVTVKAHKDNGETVTFTARVRIDTPK 863 Query: 844 EVSIYEAGGVL 854 E GGVL Sbjct: 864 EWEYNRHGGVL 874 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: 1895 Number of extensions: 85 Number of successful extensions: 8 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: 883 Length adjustment: 42 Effective length of query: 825 Effective length of database: 841 Effective search space: 693825 Effective search space used: 693825 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 24 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