Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_017598314.1 D471_RS0108975 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000341125.1:WP_017598314.1 Length = 904 Score = 701 bits (1810), Expect = 0.0 Identities = 381/873 (43%), Positives = 527/873 (60%), Gaps = 63/873 (7%) Query: 37 KLPYTSRVLAENLVRRCEPEMLTASLKQII-------ESKQELDFPWFPARVVCHDILGQ 89 +LPY+ +VL ENL+R + +TA + + + QE+ F PARV+ D G Sbjct: 32 RLPYSLKVLLENLLRTEDGANVTADHIRALGEWDAKAQPSQEIQFT--PARVIMQDFTGV 89 Query: 90 TALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRN 149 +VDLA +R+A+ GGDP ++NP+ P +L++DHS+ V+ G DAF +N IE RN Sbjct: 90 PCVVDLATMREAVRDLGGDPDKINPLAPAELVIDHSVVVDLFG-RPDAFERNVEIEYERN 148 Query: 150 EDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPH 209 +R+ F+ W Q AF V+P G GI+HQ N+E ++ V +RNG A+PDT VGTDSHT Sbjct: 149 YERYKFLRWGQTAFDEFKVVPPGTGIVHQANIEHLARVTMSRNGQAYPDTCVGTDSHTTM 208 Query: 210 VDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRA 269 + LG++ GVGG+EAE+ MLG+ M +P ++G +L+G+ +PG TATD+VL +TE LR Sbjct: 209 QNGLGILGWGVGGIEAEAAMLGQPISMLIPRVVGFKLSGQLKPGTTATDLVLTITEKLRE 268 Query: 270 QKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQV 329 VV ++EF+GEG ++ L +RATI NM+PEFG+TAA+F +D +T+ Y+ LTGR +QV Sbjct: 269 HGVVGKFVEFYGEGVSSVPLANRATIGNMSPEFGSTAAIFPVDDETIRYMRLTGRSEQQV 328 Query: 330 KLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV------------- 376 L E YAK G W D + Y L DL+ VV +IAGP P R+ Sbjct: 329 ALTEAYAKANGFWHDPAVEPEYSEYLELDLAEVVPSIAGPKRPQDRIALSEAKPTWRHDV 388 Query: 377 --------------PTSELAARGISGE---------VENEPGLMPDGAVIIAAITSCTNT 413 P S+ A +G + + GAV+IAAITSCTNT Sbjct: 389 HNYVSDDEAGEESFPASDAPATTANGRPHRPVKVTMADGTETEVDHGAVVIAAITSCTNT 448 Query: 414 SNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVG 473 SNP ++ A LLA+ A KGL+RKPWVKTS+APGSK V Y E + L P L+ LGF +VG Sbjct: 449 SNPSVMLGAALLAKKAVEKGLSRKPWVKTSMAPGSKVVTDYYERSGLTPYLDKLGFNLVG 508 Query: 474 FACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAY 533 + CTTC G SG L I + V D DL TAVLSGNRNF+GRI+P K +LASPPLVVAY Sbjct: 509 YGCTTCIGNSGPLPEEISKAVQDNDLAVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAY 568 Query: 534 AIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLS 593 A+AG++ DI + LG+ DGKPV L +IWPS EI V+ A++ + + Y +F Sbjct: 569 ALAGSLDVDITTEPLGVGSDGKPVYLADIWPSAEEIQEVMDAAIASDMYESAYADVFAGD 628 Query: 594 VDYGDKVSP---LYDWRPQSTYIRRPPYWEGAL---AGERTLKGMRPLAVLGDNITTDHL 647 + +P ++W +STY+R+PPY+EG + + G R LA LGD++TTDH+ Sbjct: 629 ERWRSLPTPTGNTFEWEDESTYVRKPPYFEGMATTPSAVTDITGARVLAKLGDSVTTDHI 688 Query: 648 SPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKV 707 SP+ AI + A EYL G+ DFNSY + RG+H R TFAN +L+N++A Sbjct: 689 SPAGAIKPGTPAAEYLKSHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIA----PG 744 Query: 708 KQGSLAR--IEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE 765 +G R +PE V+ +++A + Y + PL+++ G +YG GSSRDWAAKG RL GV Sbjct: 745 TEGGYTRDFTQPEAPVSFIYDAAQNYAAQDIPLVVLGGKEYGSGSSRDWAAKGTRLLGVR 804 Query: 766 AIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSI---APRADLTVI 822 A++ E +ERIHR+NL+GMGVLPL+F G++ + G+ G E F + G R TV Sbjct: 805 AVITESYERIHRSNLIGMGVLPLQFPEGQSADSLGLTGEETFSITGVTELNEGRVPSTVK 864 Query: 823 ITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855 ++ G VE R+DT E Y GG+LQ Sbjct: 865 VSTDTG--VEFDAVVRIDTPGEADYYRNGGILQ 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: 1966 Number of extensions: 96 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 867 Length of database: 904 Length adjustment: 43 Effective length of query: 824 Effective length of database: 861 Effective search space: 709464 Effective search space used: 709464 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 Apr 09 2024. 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