Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate BPHYT_RS04450 BPHYT_RS04450 UDP-glucose 4-epimerase
Query= metacyc::BSU38860-MONOMER (339 letters) >FitnessBrowser__BFirm:BPHYT_RS04450 Length = 340 Score = 448 bits (1153), Expect = e-131 Identities = 215/333 (64%), Positives = 258/333 (77%) Query: 3 ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62 ILVTGGAG+IGSHTCVELLN GY++VV+DNL NS+ E+L RV++ITGK +TFYEAD D Sbjct: 7 ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVNSNRESLRRVEKITGKAVTFYEADARDE 66 Query: 63 EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122 A++ +F + I IHFA LKAVGESVA P++YY NN+ L M VK+ VFS Sbjct: 67 AALNRIFDAHPITGAIHFAALKAVGESVAKPIEYYSNNVGSLLTLLGVMRDRNVKQFVFS 126 Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182 SSATVYGVP++SPI E FPL ATNPYGQ+KL+ EQ+LRDL AD W +A LRYFNP GA Sbjct: 127 SSATVYGVPKSSPIDESFPLSATNPYGQSKLIAEQVLRDLELADPSWRIATLRYFNPVGA 186 Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242 H SG IGEDP GIPNNLMPYVAQVAVGKLE+L VFG DY T DGTGVRDYIHVVDLA GH Sbjct: 187 HESGLIGEDPAGIPNNLMPYVAQVAVGKLEKLRVFGGDYETPDGTGVRDYIHVVDLARGH 246 Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302 + AL+ ++ + NLGTG GYSV+++VKAFEK +G+ VPY RRPGD+A+CFADP Sbjct: 247 LAALDALVKRDASFVVNLGTGQGYSVIDVVKAFEKAAGRPVPYEIVARRPGDVASCFADP 306 Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335 A A++ +GW A+ G+E MCAD WRWQS+N G+ Sbjct: 307 AAAEKIIGWRAQFGIERMCADHWRWQSTNPQGF 339 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: 443 Number of extensions: 8 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: 340 Length adjustment: 28 Effective length of query: 311 Effective length of database: 312 Effective search space: 97032 Effective search space used: 97032 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 BPHYT_RS04450 BPHYT_RS04450 (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.3905.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-137 442.9 0.0 3.2e-137 442.8 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS04450 BPHYT_RS04450 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS04450 BPHYT_RS04450 UDP-glucose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.8 0.0 3.2e-137 3.2e-137 2 331 .. 7 338 .. 6 339 .. 0.99 Alignments for each domain: == domain 1 score: 442.8 bits; conditional E-value: 3.2e-137 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleee 69 iLvtGgaG+iGsh++++ll+ g++vvv+Dnl+++++e+l+++ekit +v+++e+d +d+++l+++++++ lcl|FitnessBrowser__BFirm:BPHYT_RS04450 7 ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVNSNRESLRRVEKITgkAVTFYEADARDEAALNRIFDAH 76 9********************************************9999********************* PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139 i iHfaal+avgEsv++P++YY+nnv + l+Ll +m++ +vk+++Fsssa+vYg ++++pi E++pl lcl|FitnessBrowser__BFirm:BPHYT_RS04450 77 PITGAIHFAALKAVGESVAKPIEYYSNNVGSLLTLLGVMRDRNVKQFVFSSSATVYGVPKSSPIDESFPL 146 ********************************************************************** PP TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkre 208 +++npYG+skl++E++l+dl+ ad++++++ LRYFn++GA+e+g iGe++ +++ +l+++va+vavgk+e lcl|FitnessBrowser__BFirm:BPHYT_RS04450 147 SATNPYGQSKLIAEQVLRDLELADPSWRIATLRYFNPVGAHESGLIGEDPAGIPnNLMPYVAQVAVGKLE 216 ******************************************************9*************** PP TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkd 278 kl++fG+dy+t+DGt+vRDyiHv Dla +Hlaal+al + + s v nlG+gqg+sv +v++a++k++g++ lcl|FitnessBrowser__BFirm:BPHYT_RS04450 217 KLRVFGGDYETPDGTGVRDYIHVVDLARGHLAALDALVKRDASFVVNLGTGQGYSVIDVVKAFEKAAGRP 286 ********************************************************************** PP TIGR01179 279 ikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331 +++e+ +rR+GD+as++ad++ +++ +gw+++++ +e ++++ w+W++++++g lcl|FitnessBrowser__BFirm:BPHYT_RS04450 287 VPYEIVARRPGDVASCFADPAAAEKIIGWRAQFG-IERMCADHWRWQSTNPQG 338 **********************************.*************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (340 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: 6.84 // [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