Align 5-deoxy-glucuronate isomerase (EC 5.3.1.-) (characterized)
to candidate WP_011842819.1 RSPH17029_RS20285 5-deoxy-glucuronate isomerase
Query= reanno::Smeli:SMc00432 (266 letters) >NCBI__GCF_000015985.1:WP_011842819.1 Length = 268 Score = 302 bits (774), Expect = 4e-87 Identities = 150/263 (57%), Positives = 186/263 (70%), Gaps = 1/263 (0%) Query: 1 MSRLLVKPKAQAGLMQEITPESAGWTYVGFALHRLQPGETAGGETGEKELCLVLVSGKAK 60 M+ LL +P G + EITP SAGW YVGF+L+RL+PGE A TG++E+ LVLV G+A Sbjct: 1 MTTLLHRPFGSHGKVHEITPASAGWRYVGFSLYRLRPGEAAAETTGDREVILVLVEGRAS 60 Query: 61 ISVDGEDFGELGERMTPFEGRP-YAVYVPKGSSWQAEAATALDLAVCSAPGGEGFKAKVI 119 +S G+D+G LGER++ FE P +++Y+P GS+WQA A TA +AVCSAPG G A+ I Sbjct: 61 VSGGGQDWGVLGERLSVFEKTPPHSLYLPDGSAWQAVAETACTIAVCSAPGRGGHAARRI 120 Query: 120 RPGTHPQMTRGKGTNTRYVTNIMPEDDGSAQSLLVVEVITPGGHTSSYPPHKHDEDNLPA 179 P RGKGTN R + NI E + SLLV EV TP GH SSYP H+HDED+ P Sbjct: 121 GPEGIVLTERGKGTNRRQIHNIAMEAEDVCDSLLVTEVFTPAGHWSSYPSHRHDEDDYPR 180 Query: 180 ESYLEETYYHRLNPPQGFAMQRVYTDDRSLDETMAVEDGDVTLVPKGYHPVAAIHGYDSY 239 +YLEETYYHRLNP GF +QRVYTDD LDETMAV+DGDV VP+G+HP A +G++ Y Sbjct: 181 ITYLEETYYHRLNPANGFGIQRVYTDDLRLDETMAVQDGDVVCVPRGHHPCGAPYGFEMY 240 Query: 240 YLNVMAGPKRIWKFHNAREHEWL 262 YLNVMAGP R W+F A E EW+ Sbjct: 241 YLNVMAGPLRKWRFVAAPEVEWI 263 Lambda K H 0.315 0.134 0.411 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: 320 Number of extensions: 12 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: 266 Length of database: 268 Length adjustment: 25 Effective length of query: 241 Effective length of database: 243 Effective search space: 58563 Effective search space used: 58563 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: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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