Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate HSERO_RS22045 HSERO_RS22045 UDP-glucose 4-epimerase
Query= metacyc::BSU38860-MONOMER (339 letters) >FitnessBrowser__HerbieS:HSERO_RS22045 Length = 336 Score = 445 bits (1145), Expect = e-130 Identities = 214/337 (63%), Positives = 268/337 (79%), Gaps = 1/337 (0%) Query: 1 MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60 M ILVTGGAGYIGSHTCVELL +G+E++V DN NSS E++ RV++ITGK L+ + D+ Sbjct: 1 MNILVTGGAGYIGSHTCVELLKAGHEVIVFDNFCNSSPESVKRVQQITGKTLSLVKGDIR 60 Query: 61 DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120 +RE ++SV E + EAVIHFAGLKAVGESV PL YY NN+ GT L EAM+ GVK IV Sbjct: 61 NREQLESVLREFKCEAVIHFAGLKAVGESVEQPLMYYDNNVVGTVRLLEAMQATGVKTIV 120 Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180 FSSSATVYG P+ P+ E PL A+NPYG++K+++E +LRD + A +W +ALLRYFNP Sbjct: 121 FSSSATVYGDPQYLPLDEAHPLSASNPYGRSKIVIEDMLRDYYRAHPDWKIALLRYFNPV 180 Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240 GAH SG IGEDP GIPNNLMP+VAQVA+G+ E+L+++G DYPT DGTGVRD+IHVVDLA Sbjct: 181 GAHESGLIGEDPGGIPNNLMPFVAQVAIGRRERLNIWGGDYPTPDGTGVRDFIHVVDLAR 240 Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300 GHV AL+ L++ A NLGTG GYSVL+++KA+EK GK +PY A+RRPGDIA+C+A Sbjct: 241 GHVAALQ-ALDAPQCFAVNLGTGVGYSVLDVLKAYEKACGKTLPYAIAERRPGDIASCYA 299 Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYKS 337 +PA+AKR+LGWEA GLE MCADSW+WQ N NG+K+ Sbjct: 300 NPAEAKRKLGWEATLGLEAMCADSWKWQQMNPNGFKA 336 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: 446 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: 339 Length of database: 336 Length adjustment: 28 Effective length of query: 311 Effective length of database: 308 Effective search space: 95788 Effective search space used: 95788 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 HSERO_RS22045 HSERO_RS22045 (UDP-glucose 4-epimerase)
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.15959.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-141 454.6 0.0 9e-141 454.4 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS22045 HSERO_RS22045 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS22045 HSERO_RS22045 UDP-glucose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 454.4 0.0 9e-141 9e-141 1 331 [. 2 333 .. 2 334 .. 0.99 Alignments for each domain: == domain 1 score: 454.4 bits; conditional E-value: 9e-141 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavl 66 +iLvtGgaGyiGsh++++ll++g+ev+v+Dn +++s e++k++++it +++lv+gd++++e+le+vl lcl|FitnessBrowser__HerbieS:HSERO_RS22045 2 NILVTGGAGYIGSHTCVELLKAGHEVIVFDNFCNSSPESVKRVQQITgkTLSLVKGDIRNREQLESVL 69 59********************************************99999***************** PP TIGR01179 67 eeekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpis 134 +e k +aviHfa+l+avgEsv++Pl YY+nnvv+t++Lleamq++gvk+++Fsssa+vYg+++ +p+ lcl|FitnessBrowser__HerbieS:HSERO_RS22045 70 REFKCEAVIHFAGLKAVGESVEQPLMYYDNNVVGTVRLLEAMQATGVKTIVFSSSATVYGDPQYLPLD 137 ******************************************************************** PP TIGR01179 135 EesplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvae 201 E++pl++ npYGrsk+++E +l+d+ +a++++k+++LRYFn++GA+e+g iGe++ +++ +l++ va+ lcl|FitnessBrowser__HerbieS:HSERO_RS22045 138 EAHPLSASNPYGRSKIVIEDMLRDYYRAHPDWKIALLRYFNPVGAHESGLIGEDPGGIPnNLMPFVAQ 205 ***********************************************************9******** PP TIGR01179 202 vavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevie 269 va+g+re+l+i+G+dypt+DGt+vRD+iHv Dla +H+aal+al + + + nlG+g g+sv++v++ lcl|FitnessBrowser__HerbieS:HSERO_RS22045 206 VAIGRRERLNIWGGDYPTPDGTGVRDFIHVVDLARGHVAALQALDA-PQCFAVNLGTGVGYSVLDVLK 272 ********************************************96.888899*************** PP TIGR01179 270 avkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331 a +k++gk++++ +a+rR+GD+as++a+++++kr+lgw+++++ Le +++++w+W++ +++g lcl|FitnessBrowser__HerbieS:HSERO_RS22045 273 AYEKACGKTLPYAIAERRPGDIASCYANPAEAKRKLGWEATLG-LEAMCADSWKWQQMNPNG 333 *******************************************.*************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (336 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.07 // [ok]
This GapMind analysis is from Sep 17 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