Align 2-methylcitrate dehydratase 2; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate WP_020175140.1 A3OQ_RS0109440 MmgE/PrpD family protein
Query= SwissProt::Q8NSL3 (504 letters) >NCBI__GCF_000385335.1:WP_020175140.1 Length = 499 Score = 636 bits (1640), Expect = 0.0 Identities = 327/499 (65%), Positives = 375/499 (75%), Gaps = 10/499 (2%) Query: 1 MINHEVRTHRSAEEFPYEEHLAHKIARVAADPVEVAADTQEMIINRIIDNASVQAASVLR 60 M ++V H +E P LA KIA VA DPVEV+AD EM INRIIDNASV ASV R Sbjct: 1 MQTYDVNVHPESERLPRHAQLAWKIAEVANDPVEVSADVTEMAINRIIDNASVAIASVNR 60 Query: 61 RPVSSARAMAQVRPVTDGRGASVFGLPG--RYAAEWAALANGTAVRELDFHDTFLAAEYS 118 PV +AR A + GA++FG P R AEWAA ANG AVRELD+HDTFLAAEYS Sbjct: 61 HPVVTARDQALAH--SRAGGATLFGSPADIRVHAEWAAWANGVAVRELDYHDTFLAAEYS 118 Query: 119 HPGDNIPPILAAAQQAGKGGKDLIRGIATGYEIQVNLVRGMCLHEHKIDHVAHLGPSAAA 178 HPGDNIPPILA AQQ + G DL+RG+ATGYEIQV+L R +CLHEHKIDHVAHLGPS AA Sbjct: 119 HPGDNIPPILAVAQQMNRSGHDLVRGLATGYEIQVDLTRSICLHEHKIDHVAHLGPSVAA 178 Query: 179 GIGTLLDLDVDTIYQAIGQALHTTTATRQSRKGAISSWKAFAPAFAGKMSIEAVDRAMRG 238 G+GTLL L+ + IYQA+ QALH TTATRQSRKG ISSWKAFAPA AGK++IEAVDR+MRG Sbjct: 179 GLGTLLGLETEVIYQAVQQALHVTTATRQSRKGEISSWKAFAPAHAGKLAIEAVDRSMRG 238 Query: 239 EGAPSPIWEGEDGVIAWLLSGLDHIYTIPLPAEGEAKRAILDTYTKEHSAEYQSQAPIDL 298 EGAPSPI+EGED +IAW+L G Y +PLP+ GEAKRAILDTYTKEHSAEYQSQA IDL Sbjct: 239 EGAPSPIYEGEDAIIAWMLDGPGAHYHVPLPSPGEAKRAILDTYTKEHSAEYQSQALIDL 298 Query: 299 ARSMGEKLAAQGLDLRDVDSIVLHTSHHTHYVIGTGSNDPQKFDPDASRETLDHSIMYIF 358 A +G+++ D V+ IV+ TSHHTHYVIGTGS DPQKFDP ASRETLDHSIMYI Sbjct: 299 AFKLGKEIT----DWEAVEEIVVETSHHTHYVIGTGSKDPQKFDPTASRETLDHSIMYIL 354 Query: 359 AVALEDRAWHHERSYAPERAHRRETIELWNKISTVEDPEWTRRYHSVDPAEKAFGARAVI 418 AVAL+D +WHH RSY PERA R +T+ LW KI TVEDP WT RYH+ DP KAFG R +I Sbjct: 355 AVALQDGSWHHVRSYLPERAQRPDTVRLWRKIKTVEDPRWTERYHTPDPTLKAFGGRIII 414 Query: 419 TFKDGTVVEDELAVADAHPLGARPFAREQYIQKFRTLAEGVVSEKEQDRFLDAAQRTHEL 478 KDGT + DELAVA+AH LGA P+ R YI+KF TL EG++ E RFL+ QR L Sbjct: 415 RLKDGTEIADELAVANAHSLGATPWKRPDYIRKFETLTEGLIEAGEAKRFLELVQRLSSL 474 Query: 479 --EDLSELNIELDADILAK 495 E+L LN+ + A LAK Sbjct: 475 KPEELLLLNVAVPAATLAK 493 Lambda K H 0.317 0.132 0.389 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: 820 Number of extensions: 33 Number of successful extensions: 3 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: 504 Length of database: 499 Length adjustment: 34 Effective length of query: 470 Effective length of database: 465 Effective search space: 218550 Effective search space used: 218550 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: 52 (24.6 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