Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_092999067.1 BLP65_RS15560 UDP-glucose 4-epimerase GalE
Query= curated2:Q9KDV3 (334 letters) >NCBI__GCF_900102855.1:WP_092999067.1 Length = 330 Score = 352 bits (903), Expect = e-102 Identities = 173/320 (54%), Positives = 216/320 (67%) Query: 1 MAILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALSDVTFYHGDIRDDQLLDTI 60 M ILV GGAGYIGSH V L + G V+V+DNL G+ A+ F D+ D LDT+ Sbjct: 1 MRILVVGGAGYIGSHMVKLLADAGHDVVVVDNLTAGYRDAVIAGDFIQADLADRASLDTV 60 Query: 61 FTTHSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAATY 120 + S D V+HFA+ VGESV P +YY+NNV T LL M+E+ ++ +FSSTAA + Sbjct: 61 LGSGSFDGVMHFASYIQVGESVTAPAKYYQNNVANTLNLLDAMVEYGIRNFIFSSTAAVF 120 Query: 121 GEPVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGRIG 180 GEP IP+ E P P NPYG TKL +E++ AYGL+ VCLRYFNAAGA P G +G Sbjct: 121 GEPDYIPLDELHPKNPVNPYGRTKLMVEQILKDYDTAYGLKSVCLRYFNAAGAHPEGLLG 180 Query: 181 EDHSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEHLR 240 E H PE+HLIP+VLQ A G+R+ + +FG DY T DG+CIRDYIHVMDL +AH LA E L Sbjct: 181 ERHDPETHLIPLVLQAASGRRDAIKVFGQDYPTPDGTCIRDYIHVMDLCDAHLLALEKLI 240 Query: 241 KDGQSGSFNLGNGKGFSVKEVIEVCRQVTGHPIPAEIAPRRSGDPASLIASSEKAQTILG 300 G+S +FNLGNG GFSV+EVI+ +V+G IP A RRSGDPA L+A S KA+ +LG Sbjct: 241 THGKSEAFNLGNGNGFSVQEVIDTAEKVSGREIPVIAAERRSGDPARLVADSRKARELLG 300 Query: 301 WEPKYPSLETMVEHAWNWHK 320 WEP + L +V HAW W K Sbjct: 301 WEPHHADLAQIVAHAWEWEK 320 Lambda K H 0.317 0.135 0.411 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: 417 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: 334 Length of database: 330 Length adjustment: 28 Effective length of query: 306 Effective length of database: 302 Effective search space: 92412 Effective search space used: 92412 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_092999067.1 BLP65_RS15560 (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.31708.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-141 456.8 0.0 2.1e-141 456.5 0.0 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092999067.1 BLP65_RS15560 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092999067.1 BLP65_RS15560 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.5 0.0 2.1e-141 2.1e-141 1 328 [. 2 322 .. 2 325 .. 0.99 Alignments for each domain: == domain 1 score: 456.5 bits; conditional E-value: 2.1e-141 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 +iLv+GgaGyiGsh+v+ l ++g++vvv+Dnl+ g ++a+ a++ ++++dlad+++l++vl + lcl|NCBI__GCF_900102855.1:WP_092999067.1 2 RILVVGGAGYIGSHMVKLLADAGHDVVVVDNLTAGYRDAVIAGD------FIQADLADRASLDTVLGSG 64 69*****************************************9......******************* PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 ++d v+Hfa++i+vgEsv++P+kYY+nnv ntl+Ll+am+++g++++iFss+aav+ge++ +p+ E +p lcl|NCBI__GCF_900102855.1:WP_092999067.1 65 SFDGVMHFASYIQVGESVTAPAKYYQNNVANTLNLLDAMVEYGIRNFIFSSTAAVFGEPDYIPLDELHP 133 ********************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 np+npYGr+klmvE+ilkd+ +a ++lk v LRYFn+aGA++eg +Ge++ ++thli+lv+++a+g+r lcl|NCBI__GCF_900102855.1:WP_092999067.1 134 KNPVNPYGRTKLMVEQILKDYDTA-YGLKSVCLRYFNAAGAHPEGLLGERHDPETHLIPLVLQAASGRR 201 *********************999.******************************************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 +++++fG+dypt+DGtc+RDyiHv+Dl +aHl ale+l + g+se++nlG+g+gfsv+evi++++kvsg lcl|NCBI__GCF_900102855.1:WP_092999067.1 202 DAIKVFGQDYPTPDGTCIRDYIHVMDLCDAHLLALEKLITHGKSEAFNLGNGNGFSVQEVIDTAEKVSG 270 ********************************************************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328 ++i+v a+rR+GDpa+lvad+ k+++ lgw+p++ dL++i++ aw+Wek+ lcl|NCBI__GCF_900102855.1:WP_092999067.1 271 REIPVIAAERRSGDPARLVADSRKARELLGWEPHHADLAQIVAHAWEWEKHF 322 *************************************************985 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: 6.78 // [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