Align 5-deoxy-glucuronate isomerase (EC 5.3.1.-) (characterized)
to candidate 3607871 Dshi_1279 Myo-inositol catabolism IolB domain protein (RefSeq)
Query= reanno::Smeli:SMc00432 (266 letters) >FitnessBrowser__Dino:3607871 Length = 270 Score = 281 bits (720), Expect = 8e-81 Identities = 138/263 (52%), Positives = 177/263 (67%), Gaps = 1/263 (0%) Query: 1 MSRLLVKPKAQAGLMQEITPESAGWTYVGFALHRLQPGETAGGETGEKELCLVLVSGKAK 60 M LL +P A G + I+PE+AGW+YVGF L+ L PG++A TG++E LVLV G+A+ Sbjct: 1 MPDLLRRPSASTGKVHAISPEAAGWSYVGFDLYHLAPGDSAAQATGDREAILVLVEGRAE 60 Query: 61 ISVDGEDFGELGERMTPFEGRP-YAVYVPKGSSWQAEAATALDLAVCSAPGGEGFKAKVI 119 I+ G+ FGE+G+RM F+ P + +Y+P GS W A A T LAVC+AP + + Sbjct: 61 ITGGGQAFGEMGQRMNVFDKTPPHCLYIPGGSDWTATATTPCTLAVCTAPARGNHPVRRL 120 Query: 120 RPGTHPQMTRGKGTNTRYVTNIMPEDDGSAQSLLVVEVITPGGHTSSYPPHKHDEDNLPA 179 P + RG+G N R++ NI ED A SLLV EV TP G+ SSYP H+HDED+ P Sbjct: 121 GPEGIEMVPRGRGANLRHIHNIAMEDRDVAGSLLVTEVFTPAGNWSSYPSHRHDEDDFPR 180 Query: 180 ESYLEETYYHRLNPPQGFAMQRVYTDDRSLDETMAVEDGDVTLVPKGYHPVAAIHGYDSY 239 +YLEETYYHRLNP GF MQRVYTDD SLD MAV+DGDV LVP+G+HP AA +G + Y Sbjct: 181 ITYLEETYYHRLNPATGFGMQRVYTDDLSLDAAMAVQDGDVVLVPRGHHPCAAPYGIEMY 240 Query: 240 YLNVMAGPKRIWKFHNAREHEWL 262 YLNVMAGP+R W+F W+ Sbjct: 241 YLNVMAGPRRNWRFELDPNLAWI 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: 310 Number of extensions: 20 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: 270 Length adjustment: 25 Effective length of query: 241 Effective length of database: 245 Effective search space: 59045 Effective search space used: 59045 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 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