Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_077243409.1 B1A74_RS00110 UDP-glucose 4-epimerase GalE
Query= curated2:Q59083 (348 letters) >NCBI__GCF_001995255.1:WP_077243409.1 Length = 342 Score = 350 bits (898), Expect = e-101 Identities = 186/322 (57%), Positives = 221/322 (68%), Gaps = 2/322 (0%) Query: 10 RVLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRV 69 ++LVTGGAGYIGSHV+ L +AG D+LS G A+ A LV D+ +E L RV Sbjct: 2 KLLVTGGAGYIGSHVVRHLREAGHAVTVYDNLSTGHAWAVGDA-ELVVADLADSESLWRV 60 Query: 70 MRDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVY 129 + + V+HFA IVVPESV +PL YY NNT N+L LL C G+ VFSSTAAVY Sbjct: 61 LA-RGFEGVLHFAAHIVVPESVAEPLKYYDNNTRNTLNLLRGCADTGVGYFVFSSTAAVY 119 Query: 130 GAPESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTG 189 G P++ + EDAP PINPYGASK+M+E+ML D GAA LR V LRYFNVAGADP GR G Sbjct: 120 GIPDTSAVAEDAPLQPINPYGASKMMSERMLMDLGAASRLRYVSLRYFNVAGADPRGRLG 179 Query: 190 QATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLR 249 QATP ATHLIKVACQA +R + +FGTDYDT DGTC RDYIHV DLA AHV AL L+ Sbjct: 180 QATPDATHLIKVACQAATAQRDGITVFGTDYDTRDGTCERDYIHVEDLAAAHVRALEFLQ 239 Query: 250 RGGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLG 309 RGG S ++NCGYG G SV EV+ ++ SG TF RR GDPP L+A A+RIR L Sbjct: 240 RGGDSQVLNCGYGHGYSVLEVLDAVKRASGVDFAVTFGGRREGDPPALLANAERIRGTLV 299 Query: 310 WVPKHDRLDGIVRSALSWERSL 331 W P++ LD IVR AL+WE + Sbjct: 300 WQPQYANLDLIVRHALAWEEKV 321 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: 354 Number of extensions: 18 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 WP_077243409.1 B1A74_RS00110 (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.32428.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-138 445.2 0.0 6.4e-138 445.1 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077243409.1 B1A74_RS00110 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_077243409.1 B1A74_RS00110 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.1 0.0 6.4e-138 6.4e-138 1 329 [. 2 322 .. 2 325 .. 0.99 Alignments for each domain: == domain 1 score: 445.1 bits; conditional E-value: 6.4e-138 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 k+LvtGgaGyiGshvvr+l+e+g+ v v+Dnls+g+++a+ + e lv +dlad+e+l +vl++ lcl|NCBI__GCF_001995255.1:WP_077243409.1 2 KLLVTGGAGYIGSHVVRHLREAGHAVTVYDNLSTGHAWAVGDAE------LVVADLADSESLWRVLAR- 63 69****************************************99......****************86. PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 ++ v+Hfaa i v+Esv+ePlkYY+nn+ ntl+Ll+ ++++gv ++Fss+aavYg ++++++ E++p lcl|NCBI__GCF_001995255.1:WP_077243409.1 64 GFEGVLHFAAHIVVPESVAEPLKYYDNNTRNTLNLLRGCADTGVGYFVFSSTAAVYGIPDTSAVAEDAP 132 79******************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 l+pinpYG+sk+m+Er+l dl a ++l++v+LRYFnvaGAd+ g++G+a+++athlik+++++a+ +r lcl|NCBI__GCF_001995255.1:WP_077243409.1 133 LQPINPYGASKMMSERMLMDLGAA-SRLRYVSLRYFNVAGADPRGRLGQATPDATHLIKVACQAATAQR 200 *********************999.******************************************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 + +++fGtdy+t+DGtc RDyiHveDla+aH++ale l++gg+s+v+n+G+g+g+sv+ev++avk++sg lcl|NCBI__GCF_001995255.1:WP_077243409.1 201 DGITVFGTDYDTRDGTCERDYIHVEDLAAAHVRALEFLQRGGDSQVLNCGYGHGYSVLEVLDAVKRASG 269 ********************************************************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329 +d++v++ rR+GDp++l+a+a++i+ +l w+p+y +L+ i++ a++We+k lcl|NCBI__GCF_001995255.1:WP_077243409.1 270 VDFAVTFGGRREGDPPALLANAERIRGTLVWQPQYANLDLIVRHALAWEEKVA 322 *************************************************9875 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.10 // [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