Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate AO353_00880 AO353_00880 2-methylcitrate dehydratase
Query= BRENDA::P74840 (483 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00880 Length = 494 Score = 600 bits (1547), Expect = e-176 Identities = 306/492 (62%), Positives = 370/492 (75%), Gaps = 16/492 (3%) Query: 5 ELNIRPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPI 64 +LNIRPD+D+ + DI DYV+N++I SK A DTA CL+DTLGCGL AL +P C K LGPI Sbjct: 6 DLNIRPDYDKVLQDIADYVLNFKIESKEALDTARNCLMDTLGCGLLALRFPECTKHLGPI 65 Query: 65 VPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATA 124 V GTVVP GARVPGT F+LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGGILA A Sbjct: 66 VEGTVVPFGARVPGTHFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVA 125 Query: 125 DWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVASTAVVA 184 D LS+ VA G APLTM+ VL MI AHEIQG IALEN+FNRVGLDHVLLVKVASTAV A Sbjct: 126 DHLSQKRVANGDAPLTMRAVLDAMIMAHEIQGVIALENSFNRVGLDHVLLVKVASTAVTA 185 Query: 185 EMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEM 244 +++G R+++L A+S A+VDGQ+LRTYRHAPN G+RKSWAAGDA+SR VRLA +A GEM Sbjct: 186 KLMGANREQLLAALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEM 245 Query: 245 GYPSALTAKTWGFYDVSFK------------GETFRFQRPYGSYVMENVLFKISFPAEFH 292 G P LTA WGFYDV F TF + YG+YVMENVLFKISFPAEFH Sbjct: 246 GIPGVLTAPQWGFYDVLFSHTNKDLALKPADKRTFSLSQKYGTYVMENVLFKISFPAEFH 305 Query: 293 SQTAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMV 352 +QTA EAA+TL+ Q+ +I+K+ I THE+ +RII K G L N ADRDHCIQYM Sbjct: 306 AQTACEAAVTLHPQV---SNRLDEIDKIVITTHESAIRIISKVGQLANAADRDHCIQYMT 362 Query: 353 AVPLLFGRLTAADYEDEV-AQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEF 411 AVPL FG L A YED+ A ID LR+K+V EDP +T +Y + +KR+I NA+ V F Sbjct: 363 AVPLAFGTLVAEQYEDQFHAAHPIIDELRKKMVIVEDPRYTREYLEADKRSIANALQVFF 422 Query: 412 TDGSRFGEVVVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQ 471 DGS G+VVVEYPIGH RRRA+GIP L +KFK NLA +F ++ +I + D+A+LE Sbjct: 423 KDGSSTGQVVVEYPIGHRRRRAEGIPLLEDKFKANLATRFTAQRSAQIFALCQDQAKLEA 482 Query: 472 MPVNEYLDLYVI 483 PVN ++DL+VI Sbjct: 483 TPVNRFMDLFVI 494 Lambda K H 0.321 0.136 0.408 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: 658 Number of extensions: 20 Number of successful extensions: 4 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: 483 Length of database: 494 Length adjustment: 34 Effective length of query: 449 Effective length of database: 460 Effective search space: 206540 Effective search space used: 206540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 52 (24.6 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