Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate H281DRAFT_00074 H281DRAFT_00074 UDP-galactose 4-epimerase
Query= metacyc::BSU38860-MONOMER (339 letters) >FitnessBrowser__Burk376:H281DRAFT_00074 Length = 340 Score = 440 bits (1131), Expect = e-128 Identities = 211/334 (63%), Positives = 254/334 (76%) Query: 3 ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62 ILVTGGAG+IGSHTCVELLN GY++VV+DNL +S+ E+L RV+ I G+ + FYEAD D Sbjct: 7 ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVHSNRESLQRVERIAGRGVAFYEADARDE 66 Query: 63 EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122 A++ VF + I IHFA LKAVGESVA P++YY NN+ L M VK+ VFS Sbjct: 67 AALNRVFDAHPITGAIHFAALKAVGESVAKPIEYYSNNVGSLLALLGVMRDRNVKQFVFS 126 Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182 SSATVYGVP++SPI E FPL ATNPYGQ+KL+ EQ+LRDL AD W +A LRYFNP GA Sbjct: 127 SSATVYGVPKSSPIDESFPLSATNPYGQSKLIAEQVLRDLEVADPSWRIATLRYFNPVGA 186 Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242 H SG IGEDP G+PNNLMPYVAQVAVGKL++L VFG DY T DGTGVRDYIHVVDLA GH Sbjct: 187 HESGLIGEDPAGVPNNLMPYVAQVAVGKLDKLRVFGGDYETPDGTGVRDYIHVVDLARGH 246 Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302 + AL+ ++ + NLGTG GYSV+++VKAFEK SG+ VPY RRPGD+A+CFADP Sbjct: 247 LAALDALVKRDASFVVNLGTGQGYSVIDVVKAFEKASGRPVPYEIVARRPGDVASCFADP 306 Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336 A LGW A+ G+E MCAD WRWQS+N +G++ Sbjct: 307 RAALELLGWRAEFGIERMCADHWRWQSANPDGFR 340 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: 433 Number of extensions: 7 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: 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 H281DRAFT_00074 H281DRAFT_00074 (UDP-galactose 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.11530.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-136 438.3 0.0 8.2e-136 438.1 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00074 H281DRAFT_00074 UDP-galactose 4- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00074 H281DRAFT_00074 UDP-galactose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.1 0.0 8.2e-136 8.2e-136 2 330 .. 7 337 .. 6 339 .. 0.99 Alignments for each domain: == domain 1 score: 438.1 bits; conditional E-value: 8.2e-136 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleav 65 iLvtGgaG+iGsh++++ll+ g++vvv+Dnl+++++e+l+++e+i v+++e+d +d+++l++v lcl|FitnessBrowser__Burk376:H281DRAFT_00074 7 ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVHSNRESLQRVERIAgrGVAFYEADARDEAALNRV 72 9********************************************9989***************** PP TIGR01179 66 leeekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekv 131 ++++ i iHfaal+avgEsv++P++YY+nnv + l Ll +m++ +vk+++Fsssa+vYg ++++ lcl|FitnessBrowser__Burk376:H281DRAFT_00074 73 FDAHPITGAIHFAALKAVGESVAKPIEYYSNNVGSLLALLGVMRDRNVKQFVFSSSATVYGVPKSS 138 ****************************************************************** PP TIGR01179 132 pisEesplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hli 196 pi E++pl+++npYG+skl++E++l+dl+ ad++++++ LRYFn++GA+e+g iGe++ + + +l+ lcl|FitnessBrowser__Burk376:H281DRAFT_00074 139 PIDESFPLSATNPYGQSKLIAEQVLRDLEVADPSWRIATLRYFNPVGAHESGLIGEDPAGVPnNLM 204 **************************************************************9*** PP TIGR01179 197 klvaevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgf 262 ++va+vavgk++kl++fG+dy+t+DGt+vRDyiHv Dla +Hlaal+al + + s v nlG+gqg+ lcl|FitnessBrowser__Burk376:H281DRAFT_00074 205 PYVAQVAVGKLDKLRVFGGDYETPDGTGVRDYIHVVDLARGHLAALDALVKRDASFVVNLGTGQGY 270 ****************************************************************** PP TIGR01179 263 svkevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328 sv +v++a++k+sg+++++e+ +rR+GD+as++ad+ + + lgw+++++ +e ++++ w+W++ + lcl|FitnessBrowser__Burk376:H281DRAFT_00074 271 SVIDVVKAFEKASGRPVPYEIVARRPGDVASCFADPRAALELLGWRAEFG-IERMCADHWRWQSAN 335 **************************************************.************998 PP TIGR01179 329 ke 330 ++ lcl|FitnessBrowser__Burk376:H281DRAFT_00074 336 PD 337 76 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.76 // [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