Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate WP_013091230.1 BC1002_RS16990 phosphoenolpyruvate mutase
Query= SwissProt::P54528 (301 letters) >NCBI__GCF_000092885.1:WP_013091230.1 Length = 575 Score = 120 bits (300), Expect = 1e-31 Identities = 84/246 (34%), Positives = 135/246 (54%), Gaps = 11/246 (4%) Query: 15 AGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTASRGLPDLGIITSAEI 74 + R R+++ + ++ + AH+G++A + +EAGF AI+ SG A +A G+ D + ++ Sbjct: 14 SARLRQMLVSSELEFMMEAHNGLSARIVREAGFKAIWGSGLAISAQFGVRDNNEASWTQV 73 Query: 75 AERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQMEDQQLPKKCGHLNG 134 + + + A+DLP+L+D DTG+G N R R++ + +A V +ED+Q PK +NG Sbjct: 74 VDTLEFMADASDLPILLDGDTGYGNFNNVRRLVRKLEQRGIAGVCIEDKQFPKTNSFING 133 Query: 135 --KQLVPIKEMAQKIKAIK--QAAPSLIVVARTDAR-AQEGLDAAIKRSEAYIEAGADAI 189 + L I E KIKA K Q +VAR +A A G+D A++R+EAY AGADAI Sbjct: 134 EAQPLADIDEFCGKIKAGKDSQNDEHFSIVARVEALIAGWGMDEALRRAEAYRRAGADAI 193 Query: 190 FPEA-LQAENEFRQFAERIP--VPLLANMTEFGKTPYYRADEFEDMGFHMVIYPVTSLRA 246 + L +E +FA PL+ T++ TP + F + G VI+ +RA Sbjct: 194 LIHSKLSRPDEILEFAREWAGRAPLVIVPTKYYSTP---TEVFREAGISTVIWANHLIRA 250 Query: 247 AAKACE 252 A A + Sbjct: 251 ATSAMQ 256 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: 331 Number of extensions: 11 Number of successful extensions: 2 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: 575 Length adjustment: 31 Effective length of query: 270 Effective length of database: 544 Effective search space: 146880 Effective search space used: 146880 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: 50 (23.9 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