Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_092482776.1 BM299_RS07115 UDP-glucose 4-epimerase GalE
Query= SwissProt::Q7WTB1 (330 letters) >NCBI__GCF_900115975.1:WP_092482776.1 Length = 328 Score = 325 bits (834), Expect = 7e-94 Identities = 160/327 (48%), Positives = 220/327 (67%), Gaps = 1/327 (0%) Query: 1 MKVLVIGGAGYIGSHAVRELVKEGNDVLVLDALYTGHRKAVDPKAKFYQGDIEDTFLVSK 60 M +LV GGAGYIGSH V+EL+K V+ LD L GHR+AV F QGD D LV + Sbjct: 1 MNILVTGGAGYIGSHVVKELLKRNYHVVTLDNLSKGHREAVTGGV-FVQGDCGDAALVKE 59 Query: 61 ILRDEKIDAVMHFAAYSLVPESVKKPLKYYDNNVTGMISLLQAMNDANVKYLVFSSSAAT 120 ++R+ I AV+H AA SLV ES+ +P KY NN+ I+ L A+ +A V+ + SS+AA Sbjct: 60 LVREHGISAVVHLAADSLVGESMTRPDKYCQNNLGNGINFLTALAEAGVRRFILSSTAAV 119 Query: 121 YGIPKKLPITEDTPLNPINPYGETKMMMEKIMAWADKADGIKYTALRYFNVAGASSDGSI 180 YG P+ PI E P P+N YG TK+M+E+I+ W ++A G++Y +LRYFN AGA G I Sbjct: 120 YGEPEYTPIDEAHPAQPVNVYGGTKLMLEQILRWYERAYGLRYVSLRYFNAAGADPGGRI 179 Query: 181 GEDHAPETHLIPNILKSAISGDGKFTIFGDDYDTKDGTNVRDYVQVEDLIDAHILALKHM 240 GEDH PETHLIP ++++A+ K I+G DY T DGT VRDY+ V DL AHILAL+ + Sbjct: 180 GEDHDPETHLIPLVMQAALGQRDKIVIYGTDYPTPDGTCVRDYIHVSDLAVAHILALEAL 239 Query: 241 MKTNKSDVFNLGTAHGYSNLEILESAKKVTGIDIPYTMGPRRGGDPDSLVADSTKARTVL 300 S V+NLG G+S E++E+A++VTG+D GPRR GDP LVA S + + L Sbjct: 240 RDGGPSAVYNLGNERGHSVREVVETARRVTGVDFVVEEGPRREGDPAVLVAGSGRIQRDL 299 Query: 301 GWKPKHENVDDVIATAWKWHKSHPKGY 327 GW+P++ +++++ TAW+WH+ HP+GY Sbjct: 300 GWRPRYGELEEIVRTAWEWHRGHPRGY 326 Lambda K H 0.315 0.134 0.395 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: 362 Number of extensions: 15 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: 330 Length of database: 328 Length adjustment: 28 Effective length of query: 302 Effective length of database: 300 Effective search space: 90600 Effective search space used: 90600 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_092482776.1 BM299_RS07115 (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.2637.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-134 434.3 0.0 1.4e-134 434.1 0.0 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092482776.1 BM299_RS07115 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092482776.1 BM299_RS07115 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.1 0.0 1.4e-134 1.4e-134 1 331 [. 2 325 .. 2 326 .. 0.99 Alignments for each domain: == domain 1 score: 434.1 bits; conditional E-value: 1.4e-134 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 +iLvtGgaGyiGshvv++ll+++++vv+lDnlskg++ea++ + +v+gd d++ ++++++e+ lcl|NCBI__GCF_900115975.1:WP_092482776.1 2 NILVTGGAGYIGSHVVKELLKRNYHVVTLDNLSKGHREAVTGGV------FVQGDCGDAALVKELVREH 64 59***************************************999......******************* PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 i av+H+aa vgEs+++P kY +nn+ n ++ l a+++agv+++i ss+aavYge+e +pi E++p lcl|NCBI__GCF_900115975.1:WP_092482776.1 65 GISAVVHLAADSLVGESMTRPDKYCQNNLGNGINFLTALAEAGVRRFILSSTAAVYGEPEYTPIDEAHP 133 ********************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 +p+n+YG +klm+E+il+ +++a ++l++v+LRYFn+aGAd+ g+iGe++ ++thli+lv+++a+g+r lcl|NCBI__GCF_900115975.1:WP_092482776.1 134 AQPVNVYGGTKLMLEQILRWYERA-YGLRYVSLRYFNAAGADPGGRIGEDHDPETHLIPLVMQAALGQR 201 ************************.******************************************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 +k+ i+Gtdypt+DGtcvRDyiHv+Dla aH+ aleal +gg s+vynlG+ +g+sv+ev+e++++v+g lcl|NCBI__GCF_900115975.1:WP_092482776.1 202 DKIVIYGTDYPTPDGTCVRDYIHVSDLAVAHILALEALRDGGPSAVYNLGNERGHSVREVVETARRVTG 270 ********************************************************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331 +d+ ve+ +rR+GDpa+lva + +i+r lgw+p+y++Leei+++aw+W++ +++g lcl|NCBI__GCF_900115975.1:WP_092482776.1 271 VDFVVEEGPRREGDPAVLVAGSGRIQRDLGWRPRYGELEEIVRTAWEWHRGHPRG 325 *************************************************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (328 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.74 // [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