Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000009985.1:WP_011386009.1 Length = 903 Score = 677 bits (1746), Expect = 0.0 Identities = 381/876 (43%), Positives = 527/876 (60%), Gaps = 41/876 (4%) Query: 26 AIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-LKQII----ESKQELDFPWFPAR 80 A++A+ G ++LP + R++ E+++R C+ + +T ++Q+ ++ + + P+ AR Sbjct: 27 ALDAVTDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLANWRPDAPRTQEIPFVVAR 86 Query: 81 VVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAK 140 +V D G L DLA +R A G +P + P+VP L+VDHS+ V++ G + D+ Sbjct: 87 IVLQDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVVDHSVQVDHYG-EADSLDL 145 Query: 141 NRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTL 200 N E +RN +R+ FI W +AF V+P G GI+HQ+NLE ++ + ++G+ +PDTL Sbjct: 146 NMRREFQRNAERYRFIKWGMQAFDTFRVVPPGIGIVHQVNLEFLARGVLEKDGITYPDTL 205 Query: 201 VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIV 260 VGTDSHT ++ALGV GVGG+EAE+ MLG+ PD++GV L G+ G TATD+V Sbjct: 206 VGTDSHTTMINALGVAGWGVGGIEAEAGMLGQPLVFLTPDVVGVHLHGRLPEGATATDLV 265 Query: 261 LALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLT 320 L LTE LR KVV ++EFFGEG +L + DRATI+NM PE+GAT F +D++T+ YL Sbjct: 266 LFLTERLRRAKVVGKFVEFFGEGTRSLAVPDRATIANMAPEYGATMGFFPVDKETVRYLE 325 Query: 321 LTGREAEQVKLVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVRTIAGPSNPHARVPTS 379 TGR ++++ Y GL+ + + Y + FDL SV +IAGP P R+ S Sbjct: 326 ATGRTDSEIEVFRAYYSAQGLFGMPMPGDIDYSEVIEFDLGSVQPSIAGPKRPQDRLNLS 385 Query: 380 EL---------------------AARGISGEVENEPGL-MPDGAVIIAAITSCTNTSNPR 417 ++ A G VE + G V+IAAITSCTNTSNP Sbjct: 386 DMRRAFTSLFSAPAKDDGYGRPAEALGRRHRVETTAAADIGHGDVLIAAITSCTNTSNPG 445 Query: 418 NVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACT 477 ++AAGLLAR A A GL P VKTSLAPGS+ V YL +A LL +LESLGFG+V + CT Sbjct: 446 VMLAAGLLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKAGLLGDLESLGFGVVAYGCT 505 Query: 478 TCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 537 TC G SG L P ++Q + DL AVLSGNRNF+ RIHP K FL SPPLVVA+AIAG Sbjct: 506 TCIGNSGPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPAIKANFLMSPPLVVAFAIAG 565 Query: 538 TIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF---DLSV 594 I D+ ++ LG KDGKPV L +IWPS E+ + + PE +R++Y L Sbjct: 566 RIAIDMTQEPLGTGKDGKPVMLKDIWPSGREVADALLVATDPELYRRLYSDFVHGNPLWN 625 Query: 595 DYGDKVSPLYDWRPQSTYIRRPPYWE---GALAGERTLKGMRPLAVLGDNITTDHLSPSN 651 D + P Y W STYI PP++E AG + G R LA+ GD++TTDH+SP+ Sbjct: 626 DIPTQTGPAYAWE-TSTYIAEPPFFERFSPQPAGVGDIIGARALAIFGDSVTTDHISPAG 684 Query: 652 AIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQ 709 +I + S AG+YL G+ DFNSY RG+H R TFAN +++N M A VDG + Sbjct: 685 SIAVSSPAGQYLLAHGVAAGDFNSYGARRGNHEVMMRGTFANVRIRNLMLPAKVDGSRVE 744 Query: 710 GSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVA 769 G L +PEG +++A Y + P I+ AG +YG GSSRDWAAKG +L GV A+VA Sbjct: 745 GGLTLHQPEGSEMPIFDAASRYQEAGIPSIVFAGTEYGTGSSRDWAAKGPKLLGVRAVVA 804 Query: 770 EGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDV---IGSIAPRADLTVIITRK 826 + FERIHR+NLVGMGVLPL+F+ GE+ A+ GI G E F V G + PR ++ + I + Sbjct: 805 QSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFHVRGLSGVLRPRQEVVLEIVNR 864 Query: 827 NGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFL 862 G + + R+DTA E+ GG+L +D L Sbjct: 865 QGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLL 900 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: 1952 Number of extensions: 96 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 867 Length of database: 903 Length adjustment: 43 Effective length of query: 824 Effective length of database: 860 Effective search space: 708640 Effective search space used: 708640 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