Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate BPHYT_RS25670 BPHYT_RS25670 carboxyvinyl-carboxyphosphonate phosphorylmutase
Query= SwissProt::P54528 (301 letters) >FitnessBrowser__BFirm:BPHYT_RS25670 Length = 292 Score = 196 bits (499), Expect = 4e-55 Identities = 106/293 (36%), Positives = 162/293 (55%), Gaps = 7/293 (2%) Query: 5 VNKQSSQEELAGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTASR-GL 63 V +QS ++ L RF + +I+ PG D ++A +A GF +Y++G AS GL Sbjct: 3 VTQQSKRQALKARFAR----NEIVTAPGIFDMISAKIADSMGFECLYMTGFGTVASYLGL 58 Query: 64 PDLGIITSAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQMEDQ 123 PD G+ T ++ R + P++ D DTG+GG+LN A T R +A A +Q+EDQ Sbjct: 59 PDAGLATYTDMVNRVAAFCGGTNTPMICDADTGYGGLLNVAHTVRGYEQAGAAGIQLEDQ 118 Query: 124 QLPKKCGHLNGKQLVPIKEMAQKIKAIKQAAPS--LIVVARTDARAQEGLDAAIKRSEAY 181 + PKKCGH G++++P+ +M +KIK ++ +VARTDAR GLD A++R EAY Sbjct: 119 EFPKKCGHTPGRRVIPVDDMVRKIKVAAESRSDRDFQIVARTDARTSLGLDEALRRGEAY 178 Query: 182 IEAGADAIFPEALQAENEFRQFAERIPVPLLANMTEFGKTPYYRADEFEDMGFHMVIYPV 241 +AGAD +F E+ ++ E VPLL N+ E G+TP E E +GF + IYP Sbjct: 179 AKAGADVLFIESPESIEELETIGRTFNVPLLVNIVEGGRTPQLAPRELEKLGFSLAIYPA 238 Query: 242 TSLRAAAKACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIA 294 + A AKA + M+G + H S + M E+ + + + + A D+ A Sbjct: 239 SGFLAVAKALKEMYGQILAHRSTVAAVDAMYPFSEMCELMGFPEVWAFDRAHA 291 Lambda K H 0.318 0.133 0.370 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: 230 Number of extensions: 13 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: 301 Length of database: 292 Length adjustment: 26 Effective length of query: 275 Effective length of database: 266 Effective search space: 73150 Effective search space used: 73150 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: 48 (23.1 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