Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_036833329.1 N784_RS06120 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000775615.1:WP_036833329.1 Length = 904 Score = 708 bits (1828), Expect = 0.0 Identities = 389/896 (43%), Positives = 542/896 (60%), Gaps = 49/896 (5%) Query: 13 LPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-----LKQIIE 67 L G +Y+ + +E G ++LPY+ RVL E+++R+ + E++ K + Sbjct: 15 LNGKKYNYYKLK-TLEEAGLGKISRLPYSIRVLLESVLRQHDGEVIQKEHIEKLAKWGSK 73 Query: 68 SKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLA 127 + +D P+ P+RV+ D G A+VDLA LR A+ GG P ++NP VP L++DHS+ Sbjct: 74 EAESVDVPFKPSRVILQDFTGVPAVVDLASLRKAMVDMGGSPDKINPEVPVDLVIDHSVQ 133 Query: 128 VEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPV 187 V+ G K A N +E RN++R+ F+NW +KAF N +P GI+HQ+NLE ++ V Sbjct: 134 VDEYGTAK-ALDANMELEFERNKERYEFLNWAKKAFDNYQAVPPATGIVHQVNLEYLANV 192 Query: 188 IHARNGV-----AFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDII 242 +HA A+PDTLVGTDSHT ++ LGV+ GVGG+EAE+ MLG+ SY P++I Sbjct: 193 VHAIENEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLGQPSYFPAPEVI 252 Query: 243 GVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEF 302 GV+LTG G TATD+ L +T+ LR + VV ++EFFG G + L DRATISNM PE+ Sbjct: 253 GVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLADRATISNMAPEY 312 Query: 303 GATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGL-WSDDLKQAVYPRTLHFDLSS 361 GAT F +DQ++L+YL LTGR EQ++LVE Y K L ++ D + + + L Sbjct: 313 GATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTPDQEDPTFTDLVEIKLDE 372 Query: 362 VVRTIAGPSNPHARVPTSEL---------AARGISG------------EVENEPG---LM 397 + ++GP P +P +E+ A G G V++ G M Sbjct: 373 LEPNLSGPKRPQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVSVQHPSGKSSTM 432 Query: 398 PDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEE 457 GAV IAAITSCTNTSNP ++ AGLLA+ A KGL +VKTSLAPGSK V YLE+ Sbjct: 433 KTGAVAIAAITSCTNTSNPYVMLGAGLLAKKAVEKGLEVPEYVKTSLAPGSKVVTRYLED 492 Query: 458 ANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHP 517 + L+ LE LGF VG+ CTTC G SG L P ++Q + D DL ++VLSGNRNF+GRIHP Sbjct: 493 SGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQAIADNDLTVSSVLSGNRNFEGRIHP 552 Query: 518 YAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASV 577 K +LASPPLVVAYA+AGT+ D+ K+ LG D DGK V +IWPS EI A + V Sbjct: 553 LVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSMDEIKAEVDKHV 612 Query: 578 KPEQFRKVYEPMFDLSVDYGD---KVSPLYDWRPQSTYIRRPPYWEGAL---AGERTLKG 631 PE FRK YE +FD + + PLY+W +STYI+ PP++ G + + L G Sbjct: 613 NPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLSEDPSEVKDLDG 672 Query: 632 MRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATF 691 +R + GD++TTDH+SP+ AI D AG+YL G+ FNSY + RG+H R TF Sbjct: 673 LRVIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRRGNHEVMMRGTF 732 Query: 692 ANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSS 751 AN +++N++A +G P V +++A Y ++ L++IAG DYG GSS Sbjct: 733 ANIRIRNKIA----PGTEGGYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGNDYGMGSS 788 Query: 752 RDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFD--V 809 RDWAAKG L G++ ++AE FERIHR+NLV MGVLPL+FK G++ + G+ G E FD + Sbjct: 789 RDWAAKGTNLLGIKTVIAESFERIHRSNLVMMGVLPLQFKDGDSADSLGLSGKETFDIKI 848 Query: 810 IGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESN 865 ++ PR + VI + G + E V R D+ E+ Y GG+LQ+ +D L+SN Sbjct: 849 DETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGILQKVLRDKLQSN 904 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: 1931 Number of extensions: 102 Number of successful extensions: 9 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: 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 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