Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_045580974.1 AL072_RS06770 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_001305595.1:WP_045580974.1 Length = 896 Score = 723 bits (1867), Expect = 0.0 Identities = 393/874 (44%), Positives = 548/874 (62%), Gaps = 40/874 (4%) Query: 15 GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVR-----RCEPEMLTASLKQIIESK 69 G + DYF + A +A G ++LP++ +VL ENL+R + + A + +++ + Sbjct: 20 GKSYDYFSLKAAEQA-GLGDLSRLPFSMKVLLENLLRFEDGRTVSVDDVKAVAQWLVDKR 78 Query: 70 QELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVE 129 + + + PARV+ D G A+ DLA +R+A+AA GGDPA++NP+VP L++DHS+ V+ Sbjct: 79 SDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPAKINPLVPVDLVIDHSVMVD 138 Query: 130 YGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIH 189 Y G D+F +N +E RN +R+ F+ W QKAF N V+P G GI HQ+N E +S V+ Sbjct: 139 YFG-GADSFQRNVDLEFERNLERYEFLRWGQKAFDNFRVVPPGTGICHQVNTEYLSQVVW 197 Query: 190 -----ARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 + VA+PDTLVGTDSHT V+ L V+ GVGG+EAE+ MLG+ M +P++IG Sbjct: 198 TDADPSGRPVAYPDTLVGTDSHTTMVNGLSVLGWGVGGIEAEAAMLGQPISMLIPEVIGF 257 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 +LTG+ + G+TATD+VL +T+ LR + VV ++EFFG G +++TL DRATI NM PE+GA Sbjct: 258 KLTGRMKEGMTATDLVLTVTQMLRRKGVVGKFVEFFGPGLDSMTLPDRATIGNMAPEYGA 317 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSD-DLKQAVYPRTLHFDLSSVV 363 T +F ID +T+ YLT TGR+ +V LVE YAK G+W + D V+ L D+ +V Sbjct: 318 TCGIFPIDAETIRYLTFTGRDPGRVALVEAYAKAQGMWREPDSPDPVFSDVLELDMGTVE 377 Query: 364 RTIAGPSNPHARVPTSELA---ARGISGE-----------VENEPGLMPDGAVIIAAITS 409 ++AGP P RV S LA AR ++ V++ + GAV+IAAITS Sbjct: 378 PSLAGPKRPQDRVALSALAQGFARDMAEAYKADDPKKAVPVKDAGYSLEQGAVVIAAITS 437 Query: 410 CTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGF 469 CTNTSNP ++AAGLLA+ A KGL +KPWVKTSLAPGS+ V YL +A L P L+ LGF Sbjct: 438 CTNTSNPAVLVAAGLLAKKAVEKGLAQKPWVKTSLAPGSQVVTDYLAKAGLQPYLDRLGF 497 Query: 470 GIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 529 IVG+ CTTC G SG L I V D +L AVLSGNRNF+GR++P+ + +LASPPL Sbjct: 498 NIVGYGCTTCIGNSGPLPEPIAAAVEDGNLVVGAVLSGNRNFEGRVNPHTRANYLASPPL 557 Query: 530 VVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPM 589 VAYA+AG + D+ + LG DG+PV L +IWP++ E+ I AS+ + FR Y + Sbjct: 558 CVAYALAGNLNIDLTTEPLGTGTDGQPVYLKDIWPTNREVQDAIDASLTADMFRSRYSDV 617 Query: 590 FDLSVDY---GDKVSPLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNIT 643 F + Y W+ STY++ PP++ G L ++G R LAVLGD+IT Sbjct: 618 FKGPEQWQAIATAEGQTYQWQDASTYVKLPPFFSGLTRTLDPVSDVRGARALAVLGDSIT 677 Query: 644 TDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIV 703 TDH+SP+ +I S AGEYL + +DFNSY RG+H R TFAN +++NE+ Sbjct: 678 TDHISPAGSIKRTSPAGEYLLSHQVRLQDFNSYGARRGNHEVMMRGTFANIRIRNELL-- 735 Query: 704 DGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAG 763 +G + P G ++ A Y D PL+++AG +YG GSSRDWAAKG RL G Sbjct: 736 --PGVEGGETKHYPSGERLPIYTAAMRYADEGVPLVVVAGKEYGTGSSRDWAAKGTRLLG 793 Query: 764 VEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLT 820 ++A++AE FERIHR+NLVGMG+LPL+FK G RA +DG+E FD+ G + PR D+ Sbjct: 794 IKAVIAESFERIHRSNLVGMGILPLQFKDGLTRADLKLDGSETFDIAGIEQDLRPRKDVA 853 Query: 821 VIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854 + +TR +G + R+DT +EV Y GGVL Sbjct: 854 LTLTRADGTVEHHTLLLRIDTLDEVEYYRNGGVL 887 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: 1981 Number of extensions: 94 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: 896 Length adjustment: 43 Effective length of query: 824 Effective length of database: 853 Effective search space: 702872 Effective search space used: 702872 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