Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_012992034.1 THAL_RS05070 UDP-glucose 4-epimerase GalE
Query= curated2:Q59083 (348 letters) >NCBI__GCF_000025605.1:WP_012992034.1 Length = 327 Score = 308 bits (789), Expect = 1e-88 Identities = 163/324 (50%), Positives = 211/324 (65%), Gaps = 1/324 (0%) Query: 10 RVLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRV 69 +VLVTGGAGYIGSH++ L + G + +D+LS G+REA+ LV D+ L+ + Sbjct: 2 KVLVTGGAGYIGSHMVKLLGEKGYQVLVVDNLSTGKREAVLYG-RLVVLDLLLYAPLEEL 60 Query: 70 MRDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVY 129 M D R D VMHFA I+V ESV KPL+YY NN + LL A RAG+ ++FSS+AAVY Sbjct: 61 MLDFRPDIVMHFAAKILVHESVRKPLEYYENNLQATWNLLRAMKRAGVKYMIFSSSAAVY 120 Query: 130 GAPESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTG 189 G P S+P++E PTVPINPYG SKLM E+M+ D A GL+ ILRYFNVAGADP + G Sbjct: 121 GTPSSLPVKESDPTVPINPYGWSKLMGERMVEDFARAEGLKFGILRYFNVAGADPELKLG 180 Query: 190 QATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLR 249 THLI A + G P L ++GTDY TPDGTC+RDYIHV+DL +AH+ L +L Sbjct: 181 PVKQNPTHLIARAVKVAKGDIPYLEVYGTDYPTPDGTCVRDYIHVTDLCNAHLRVLEYLL 240 Query: 250 RGGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLG 309 GG S + N GYG+G SV EV+R ++EV+G + +RR GDPP+LVA ++ G Sbjct: 241 EGGQSDVFNVGYGKGYSVLEVIRVVKEVTGRDFEVRYTERREGDPPELVADPAKLVTLTG 300 Query: 310 WVPKHDRLDGIVRSALSWERSLEQ 333 W P D L IV++ WE LE+ Sbjct: 301 WKPSFDDLSFIVKTLWEWELILEK 324 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: 336 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: 348 Length of database: 327 Length adjustment: 28 Effective length of query: 320 Effective length of database: 299 Effective search space: 95680 Effective search space used: 95680 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_012992034.1 THAL_RS05070 (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.9033.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-132 427.5 0.0 1.7e-132 427.2 0.0 1.0 1 lcl|NCBI__GCF_000025605.1:WP_012992034.1 THAL_RS05070 UDP-glucose 4-epime Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025605.1:WP_012992034.1 THAL_RS05070 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.2 0.0 1.7e-132 1.7e-132 1 326 [. 2 320 .. 2 325 .. 0.99 Alignments for each domain: == domain 1 score: 427.2 bits; conditional E-value: 1.7e-132 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 k+LvtGgaGyiGsh+v+ l ekg++v+v+Dnls+g++ea+ +++ lv dl + le+++ + lcl|NCBI__GCF_000025605.1:WP_012992034.1 2 KVLVTGGAGYIGSHMVKLLGEKGYQVLVVDNLSTGKREAVLYGR------LVVLDLLLYAPLEELMLDF 64 79******************************************......9****************** PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 ++d v+Hfaa+i v+Esv++Pl+YYenn+++t +Ll+am++agvk +iFsssaavYg+++++p++E+ p lcl|NCBI__GCF_000025605.1:WP_012992034.1 65 RPDIVMHFAAKILVHESVRKPLEYYENNLQATWNLLRAMKRAGVKYMIFSSSAAVYGTPSSLPVKESDP 133 ********************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 + pinpYG sklm Er+++d+++a ++lk+ iLRYFnvaGAd+e ++G ++n thli ++++va g lcl|NCBI__GCF_000025605.1:WP_012992034.1 134 TVPINPYGWSKLMGERMVEDFARA-EGLKFGILRYFNVAGADPELKLGPVKQNPTHLIARAVKVAKGDI 201 ************************.******************************************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 + le++Gtdypt+DGtcvRDyiHv+Dl +aHl+ le+l egg+s+v+n+G+g+g+sv+evi+ vk+v+g lcl|NCBI__GCF_000025605.1:WP_012992034.1 202 PYLEVYGTDYPTPDGTCVRDYIHVTDLCNAHLRVLEYLLEGGQSDVFNVGYGKGYSVLEVIRVVKEVTG 270 ********************************************************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWek 326 +d++v+ ++rR+GDp++lvad++k + +gwkp++ddL i+k+ w+We lcl|NCBI__GCF_000025605.1:WP_012992034.1 271 RDFEVRYTERREGDPPELVADPAKLVTLTGWKPSFDDLSFIVKTLWEWEL 320 ************************************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (327 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: 9.69 // [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