Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_012468955.1 GLOV_RS04315 UDP-glucose 4-epimerase GalE
Query= curated2:Q59083 (348 letters) >NCBI__GCF_000020385.1:WP_012468955.1 Length = 330 Score = 338 bits (868), Expect = 9e-98 Identities = 174/324 (53%), Positives = 219/324 (67%) Query: 8 SPRVLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLD 67 S ++LVTGG GYIGSHV+ L++AG V D+LS G ++A+ L++ ++ L+ Sbjct: 2 SDKILVTGGCGYIGSHVVRQLSEAGHSVVVYDNLSTGFQDALLHGEELIQAELADHAALE 61 Query: 68 RVMRDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAA 127 + HR V+HFA +IV PESV PL YY NNT N+L LL A +R G+++ VFSSTAA Sbjct: 62 AAFQKHRFKTVLHFAAAIVAPESVSLPLKYYGNNTRNTLGLLEASVRNGVERFVFSSTAA 121 Query: 128 VYGAPESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGR 187 VYG PE E+ PINPYG SKLM+E MLRD AAHGL+ V LRYFNVAGADP R Sbjct: 122 VYGFPEGGSASEETLLAPINPYGTSKLMSEWMLRDTAAAHGLKYVALRYFNVAGADPQAR 181 Query: 188 TGQATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLH 247 GQ TP ATHLIK+ACQ LG+R AI+GTDY TPDGT IRDYIH+ DLA AH+ AL + Sbjct: 182 IGQRTPEATHLIKIACQTALGQRQQAAIYGTDYPTPDGTGIRDYIHIEDLAAAHLAALDY 241 Query: 248 LRRGGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQ 307 L +GG S +N GYG+G+SVREV+ +++VSG RRPGDP LVA A++I+ Sbjct: 242 LDKGGESTAINVGYGQGSSVREVLAMVKQVSGVDFRVVEEGRRPGDPACLVARAEKIKLL 301 Query: 308 LGWVPKHDRLDGIVRSALSWERSL 331 W P+ + L+ IV A WE SL Sbjct: 302 TDWQPRFNSLETIVEDAWRWESSL 325 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: 372 Number of extensions: 16 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_012468955.1 GLOV_RS04315 (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.24770.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-140 453.9 0.0 1.6e-140 453.6 0.0 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012468955.1 GLOV_RS04315 UDP-glucose 4-epime Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012468955.1 GLOV_RS04315 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.6 0.0 1.6e-140 1.6e-140 1 328 [. 4 325 .. 4 328 .. 0.99 Alignments for each domain: == domain 1 score: 453.6 bits; conditional E-value: 1.6e-140 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 kiLvtGg+GyiGshvvrql+e+g++vvv+Dnls+g+++al ++e +l++++lad+++lea+++++ lcl|NCBI__GCF_000020385.1:WP_012468955.1 4 KILVTGGCGYIGSHVVRQLSEAGHSVVVYDNLSTGFQDALLHGE-----ELIQAELADHAALEAAFQKH 67 79******************************************.....5******************* PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 ++++v+Hfaa i +Esv+ PlkYY nn+ ntl Llea ++ gv++++Fss+aavYg +e + sEe+ lcl|NCBI__GCF_000020385.1:WP_012468955.1 68 RFKTVLHFAAAIVAPESVSLPLKYYGNNTRNTLGLLEASVRNGVERFVFSSTAAVYGFPEGGSASEETL 136 ********************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 l+pinpYG+sklm+E++l+d++ a ++lk+v+LRYFnvaGAd++ +iG+++++athlik+++++a+g+r lcl|NCBI__GCF_000020385.1:WP_012468955.1 137 LAPINPYGTSKLMSEWMLRDTAAA-HGLKYVALRYFNVAGADPQARIGQRTPEATHLIKIACQTALGQR 204 *********************999.******************************************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 ++ +i+Gtdypt+DGt++RDyiH+eDla+aHlaal++l +gges++ n+G+gqg sv+ev+ vk+vsg lcl|NCBI__GCF_000020385.1:WP_012468955.1 205 QQAAIYGTDYPTPDGTGIRDYIHIEDLAAAHLAALDYLDKGGESTAINVGYGQGSSVREVLAMVKQVSG 273 ********************************************************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328 +d++v ++ rR+GDpa+lva a+kik ++w+p+++ Le+i+++aw+We++l lcl|NCBI__GCF_000020385.1:WP_012468955.1 274 VDFRVVEEGRRPGDPACLVARAEKIKLLTDWQPRFNSLETIVEDAWRWESSL 325 *************************************************975 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.40 // [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