Align 5-deoxy-glucuronate isomerase (EC 5.3.1.-) (characterized)
to candidate BPHYT_RS28505 BPHYT_RS28505 5-deoxyglucuronate isomerase
Query= reanno::Smeli:SMc00432 (266 letters) >FitnessBrowser__BFirm:BPHYT_RS28505 Length = 276 Score = 295 bits (755), Expect = 7e-85 Identities = 147/264 (55%), Positives = 183/264 (69%), Gaps = 3/264 (1%) Query: 1 MSRLLVKPKAQA--GLMQEITPESAGWTYVGFALHRLQPGETAGGETGEKELCLVLVSGK 58 MS LLVKP A G + ITP SAGW YVGF + L PG T +TG++E+ +VLV G Sbjct: 1 MSDLLVKPSKHAKDGQIIHITPASAGWKYVGFDVFDLVPGATVTRDTGDREVVVVLVKGH 60 Query: 59 AKISVDGEDFGELGERMTPFEGRPYAVYVPKGSSWQAEAATALDLAVCSAPGGEGFKAKV 118 A + +G E+G RM+PF+G P++VYVP + + A ++L VCSAP G + Sbjct: 61 ATVGCEGLASREIGTRMSPFDGAPWSVYVPPHTRYTIVATDDVELGVCSAPAKGGLPPRF 120 Query: 119 IRPGTHPQMTRGKGTNTRYVTNIMPEDDGSAQSLLVVEVITPGGHTSSYPPHKHDEDNLP 178 I P Q TRG G N R+V +I+PE + A+SLLVVE +TP G+ SSYPPH+HD D+ Sbjct: 121 IAPDEVKQETRGAGANLRHVRHILPETE-PAESLLVVESVTPAGNWSSYPPHRHDTDDGE 179 Query: 179 AESYLEETYYHRLNPPQGFAMQRVYTDDRSLDETMAVEDGDVTLVPKGYHPVAAIHGYDS 238 ++YLEETYYHR++PPQGFA+QRVYTDDRSLDET+A D V LVP+GYHPVAA HGYD Sbjct: 180 QQTYLEETYYHRVSPPQGFAIQRVYTDDRSLDETLAAYDKHVVLVPRGYHPVAAAHGYDL 239 Query: 239 YYLNVMAGPKRIWKFHNAREHEWL 262 YYLNVMAGP+R W HN HEWL Sbjct: 240 YYLNVMAGPRRTWHVHNEPAHEWL 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: 314 Number of extensions: 10 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: 276 Length adjustment: 25 Effective length of query: 241 Effective length of database: 251 Effective search space: 60491 Effective search space used: 60491 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