Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_085771384.1 B1812_RS09540 UDP-glucose 4-epimerase GalE
Query= curated2:Q59083 (348 letters) >NCBI__GCF_002117405.1:WP_085771384.1 Length = 330 Score = 384 bits (985), Expect = e-111 Identities = 190/321 (59%), Positives = 227/321 (70%) Query: 11 VLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRVM 70 VLVTGGAGYIGSH+ AL DAG V +D+LS G R A+P VPLV GD G +L+ + Sbjct: 3 VLVTGGAGYIGSHMALALVDAGEEVVVLDNLSTGFRWAVPEGVPLVIGDFGDEDLVTETI 62 Query: 71 RDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVYG 130 + V + HFA IVVPESV PL YY NNTA + TLL + +++ +FSSTAAVYG Sbjct: 63 ARYNVSEIAHFAAKIVVPESVADPLGYYLNNTAKARTLLETAVNCEVERFIFSSTAAVYG 122 Query: 131 APESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTGQ 190 P P+ ED P P++PYG SKLM E ML D AHGLR V+LRYFNVAG DP GR GQ Sbjct: 123 DPSKNPVDEDEPLKPVSPYGRSKLMVEWMLEDTARAHGLRYVVLRYFNVAGGDPKGRAGQ 182 Query: 191 ATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLRR 250 +TP ATHLIKVA QA LG R L +FGTDY TPDG+C+RDYI V+DLA AH+ AL HLR Sbjct: 183 STPKATHLIKVAVQAALGLRDKLQVFGTDYPTPDGSCVRDYIQVTDLAQAHLDALRHLRG 242 Query: 251 GGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLGW 310 GG +L+ NCGYGRG SV EV+ T++ V+G P A RRPGDP +VAG+ RI+E+LGW Sbjct: 243 GGDNLVCNCGYGRGFSVLEVIETVKRVAGVDFPVEIAGRRPGDPAAIVAGSARIQERLGW 302 Query: 311 VPKHDRLDGIVRSALSWERSL 331 P+HD L+ IVR AL WER L Sbjct: 303 KPQHDSLEEIVRQALEWERGL 323 Lambda K H 0.319 0.136 0.401 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: 376 Number of extensions: 10 Number of successful extensions: 1 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: 348 Length of database: 330 Length adjustment: 28 Effective length of query: 320 Effective length of database: 302 Effective search space: 96640 Effective search space used: 96640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_085771384.1 B1812_RS09540 (UDP-glucose 4-epimerase GalE)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01179.hmm # target sequence database: /tmp/gapView.18902.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01179 [M=332] Accession: TIGR01179 Description: galE: UDP-glucose 4-epimerase GalE Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-131 424.2 0.0 1.6e-131 424.0 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085771384.1 B1812_RS09540 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085771384.1 B1812_RS09540 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 424.0 0.0 1.6e-131 1.6e-131 1 328 [. 2 323 .. 2 327 .. 0.99 Alignments for each domain: == domain 1 score: 424.0 bits; conditional E-value: 1.6e-131 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 ++LvtGgaGyiGsh++ +l ++g evvvlDnls+g+++a++++ lv gd d+ +++++++ lcl|NCBI__GCF_002117405.1:WP_085771384.1 2 AVLVTGGAGYIGSHMALALVDAGEEVVVLDNLSTGFRWAVPEGV-----PLVIGDFGDEDLVTETIARY 65 59***************************************998.....8******************* PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 ++ + Hfaa+i v+Esv++Pl YY nn+ + +Lle+ ++ +v+++iFss+aavYg+++k+p+ E++p lcl|NCBI__GCF_002117405.1:WP_085771384.1 66 NVSEIAHFAAKIVVPESVADPLGYYLNNTAKARTLLETAVNCEVERFIFSSTAAVYGDPSKNPVDEDEP 134 ********************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 l+p++pYGrsklmvE++l+d+++a ++l++v+LRYFnvaG d++g+ G+++++athlik+++++a+g r lcl|NCBI__GCF_002117405.1:WP_085771384.1 135 LKPVSPYGRSKLMVEWMLEDTARA-HGLRYVVLRYFNVAGGDPKGRAGQSTPKATHLIKVAVQAALGLR 202 ************************.******************************************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 +kl++fGtdypt+DG cvRDyi v+Dla+aHl+al+ l gg+ v n+G+g+gfsv+evie+vk+v+g lcl|NCBI__GCF_002117405.1:WP_085771384.1 203 DKLQVFGTDYPTPDGSCVRDYIQVTDLAQAHLDALRHLRGGGDNLVCNCGYGRGFSVLEVIETVKRVAG 271 ********************************************************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328 +d++ve+a rR+GDpa++va +++i+++lgwkp++d Leei+++a++We+ l lcl|NCBI__GCF_002117405.1:WP_085771384.1 272 VDFPVEIAGRRPGDPAAIVAGSARIQERLGWKPQHDSLEEIVRQALEWERGL 323 ************************************************9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (330 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.72 // [ok]
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