Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate GFF2094 HP15_2048 UDP-glucose 4-epimerase
Query= curated2:Q59083 (348 letters) >FitnessBrowser__Marino:GFF2094 Length = 342 Score = 349 bits (895), Expect = e-101 Identities = 180/319 (56%), Positives = 221/319 (69%), Gaps = 1/319 (0%) Query: 10 RVLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRV 69 +VLVTGGAGYIGSHV+ L AG V D+LS G R A+ A LV GD+ ++ + Sbjct: 2 KVLVTGGAGYIGSHVVRQLGQAGHDIVVFDNLSTGYRWAVTAG-ELVVGDLADEAAIEDL 60 Query: 70 MRDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVY 129 H+ +AV+HFA +IVVPESV PL YY NNT N+L LL A + + +VFSSTAAVY Sbjct: 61 FSRHQFEAVLHFAANIVVPESVANPLKYYSNNTRNTLNLLKAVEKHEVPYMVFSSTAAVY 120 Query: 130 GAPESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTG 189 G PE + ED P PINPYGASK+M+E+M+ D AA L VILRYFNVAGA+P G G Sbjct: 121 GMPEQTVLTEDLPLAPINPYGASKMMSERMIMDLAAASSLNYVILRYFNVAGANPEGLLG 180 Query: 190 QATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLR 249 QATP ATHLIKVAC+ + +R +++FGTDYDT DGTCIRDYIHV DLA AHV+AL ++ Sbjct: 181 QATPEATHLIKVACECVTEQREGMSVFGTDYDTRDGTCIRDYIHVEDLAKAHVMALDYMA 240 Query: 250 RGGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLG 309 GG S +MNCGYGRG +VREV+ ++ SG P T RR GDP L+A IR+ LG Sbjct: 241 DGGHSKVMNCGYGRGFTVREVIDVVKAQSGVDFPVTETGRRAGDPAALMADNTLIRQTLG 300 Query: 310 WVPKHDRLDGIVRSALSWE 328 W P +D LD IV +AL+WE Sbjct: 301 WQPDYDNLDTIVGTALAWE 319 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: 364 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: 348 Length of database: 342 Length adjustment: 29 Effective length of query: 319 Effective length of database: 313 Effective search space: 99847 Effective search space used: 99847 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 GFF2094 HP15_2048 (UDP-glucose 4-epimerase)
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.30715.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-143 463.7 0.1 1.5e-143 463.5 0.1 1.0 1 lcl|FitnessBrowser__Marino:GFF2094 HP15_2048 UDP-glucose 4-epimeras Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2094 HP15_2048 UDP-glucose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.5 0.1 1.5e-143 1.5e-143 1 327 [. 2 321 .. 2 326 .. 0.99 Alignments for each domain: == domain 1 score: 463.5 bits; conditional E-value: 1.5e-143 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidavi 75 k+LvtGgaGyiGshvvrql ++g+++vv+Dnls+g ++a++a+e lv gdlad++++e+++++++++av+ lcl|FitnessBrowser__Marino:GFF2094 2 KVLVTGGAGYIGSHVVRQLGQAGHDIVVFDNLSTGYRWAVTAGE------LVVGDLADEAAIEDLFSRHQFEAVL 70 79******************************************......************************* PP TIGR01179 76 HfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrskl 150 Hfaa i v+Esv++PlkYY+nn+ ntl+Ll+a++k++v ++Fss+aavYg++e+++++E+ pl+pinpYG+sk+ lcl|FitnessBrowser__Marino:GFF2094 71 HFAANIVVPESVANPLKYYSNNTRNTLNLLKAVEKHEVPYMVFSSTAAVYGMPEQTVLTEDLPLAPINPYGASKM 145 *************************************************************************** PP TIGR01179 151 mvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDGtcv 225 m+Er++ dl+ a ++l++viLRYFnvaGA++eg +G+a+++athlik+++e+++ +re +++fGtdy+t+DGtc+ lcl|FitnessBrowser__Marino:GFF2094 146 MSERMIMDLAAA-SSLNYVILRYFNVAGANPEGLLGQATPEATHLIKVACECVTEQREGMSVFGTDYDTRDGTCI 219 *********999.************************************************************** PP TIGR01179 226 RDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadask 300 RDyiHveDla+aH+ al+++++gg+s+v n+G+g+gf v+evi+ vk+ sg+d++v+++ rRaGDpa+l+ad+ lcl|FitnessBrowser__Marino:GFF2094 220 RDYIHVEDLAKAHVMALDYMADGGHSKVMNCGYGRGFTVREVIDVVKAQSGVDFPVTETGRRAGDPAALMADNTL 294 *************************************************************************** PP TIGR01179 301 ikrelgwkpkyddLeeiiksawdWekk 327 i+++lgw+p yd+L++i+ +a++We lcl|FitnessBrowser__Marino:GFF2094 295 IRQTLGWQPDYDNLDTIVGTALAWEAI 321 ************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (342 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: 10.14 // [ok]
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