Align 5-deoxy-glucuronate isomerase (EC 5.3.1.-) (characterized)
to candidate CCNA_01359 CCNA_01359 myo-inositol catabolism protein IolB
Query= reanno::Smeli:SMc00432 (266 letters) >FitnessBrowser__Caulo:CCNA_01359 Length = 269 Score = 300 bits (768), Expect = 2e-86 Identities = 150/265 (56%), Positives = 188/265 (70%), Gaps = 4/265 (1%) Query: 1 MSRLLVKPKAQ--AGLMQEITPESAGWTYVGFALHRLQPGETAGGETGEKELCLVLVSGK 58 MS+LLV+P A G + E+TP SAGWT+VGF + +L G G ++E C+V++SG Sbjct: 2 MSKLLVRPHAPDATGSVLEVTPASAGWTHVGFQVVKLAAGAVFEGGDPDRETCIVVMSGT 61 Query: 59 AKISVDGEDFGELGERMTPFEGR-PYAVYVPKGSSWQAEAATALDLAVCSAPGGEGFKAK 117 A++S G FG +G R + FE + P AVYVP ++ A + +++A+CSAPG G +A+ Sbjct: 62 AEVSAQGVSFGAIGGRASVFEDKAPGAVYVPAAIAFSVSAVSDVEVALCSAPGQPGGQAR 121 Query: 118 VIRPGTHPQMTRGKGTNTRYVTNIMPEDDGSAQSLLVVEVITPGGHTSSYPPHKHDEDNL 177 +I P+ TRG+GTNTR+V NI+PE A LLVVEVITPGGH SSYPPHKHD Sbjct: 122 LIAEHDMPRETRGRGTNTRFVRNILPET-APADGLLVVEVITPGGHWSSYPPHKHDTAAE 180 Query: 178 PAESYLEETYYHRLNPPQGFAMQRVYTDDRSLDETMAVEDGDVTLVPKGYHPVAAIHGYD 237 E+ LEETYYHRLNPPQGFA QRVYTDDRSLDET+ V+DGDV +VP+GYHPV A HGYD Sbjct: 181 GEETALEETYYHRLNPPQGFAFQRVYTDDRSLDETVCVQDGDVVMVPRGYHPVGAPHGYD 240 Query: 238 SYYLNVMAGPKRIWKFHNAREHEWL 262 YYLNVMAGP R W F N H+W+ Sbjct: 241 LYYLNVMAGPHRKWIFRNDPAHDWI 265 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: 323 Number of extensions: 18 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: 266 Length of database: 269 Length adjustment: 25 Effective length of query: 241 Effective length of database: 244 Effective search space: 58804 Effective search space used: 58804 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