Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate 6938103 Sama_2224 UDP-glucose 4-epimerase (RefSeq)
Query= metacyc::BSU38860-MONOMER (339 letters) >FitnessBrowser__SB2B:6938103 Length = 336 Score = 487 bits (1254), Expect = e-142 Identities = 230/336 (68%), Positives = 275/336 (81%) Query: 1 MAILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLL 60 M ILVTGGAGYIG+HT V L +G E++VLDNLSN+ EALNRV++ITG+ + F + D+L Sbjct: 1 MTILVTGGAGYIGTHTVVALQQAGMEVLVLDNLSNACVEALNRVEQITGQAVPFVQGDIL 60 Query: 61 DREAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120 D+ + +F +N+IEAVIHFAGLKAVGESVA PL+YY NN+TGT +LC+ M ++ VK++V Sbjct: 61 DKPLLMKIFMDNDIEAVIHFAGLKAVGESVAQPLRYYENNVTGTLVLCQVMAEFNVKQLV 120 Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180 FSSSATVYG P + PITEDFP GATNPYGQ+KLM+E IL DLH +D W++A LRYFNP Sbjct: 121 FSSSATVYGDPASLPITEDFPTGATNPYGQSKLMVEHILADLHHSDPSWNIARLRYFNPV 180 Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240 GAH SG IGEDPN IPNNLMP+++QVAVGK E+LS+FGNDYPT DGTGVRDYIHVVDLA+ Sbjct: 181 GAHESGLIGEDPNDIPNNLMPFISQVAVGKREKLSIFGNDYPTHDGTGVRDYIHVVDLAD 240 Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300 GH+KALEK+ G YNLGTG GYSVL+MVKAFEK SGK VPY A RRPGDIA C+A Sbjct: 241 GHLKALEKLRTQPGLVTYNLGTGQGYSVLDMVKAFEKASGKAVPYEIAPRRPGDIAACYA 300 Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336 DP KA +ELGW+AK ++EM A SWRWQS N NGY+ Sbjct: 301 DPGKATKELGWKAKLSVDEMAASSWRWQSGNPNGYR 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: 476 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: 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 6938103 Sama_2224 (UDP-glucose 4-epimerase (RefSeq))
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.29752.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-146 473.7 0.0 1.4e-146 473.5 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6938103 Sama_2224 UDP-glucose 4-epimeras Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938103 Sama_2224 UDP-glucose 4-epimerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.5 0.0 1.4e-146 1.4e-146 2 331 .. 3 334 .. 2 335 .. 0.99 Alignments for each domain: == domain 1 score: 473.5 bits; conditional E-value: 1.4e-146 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeekidaviH 76 iLvtGgaGyiG h+v++l+++g+ev+vlDnls++ eal+++e+it +v +v+gd+ dk l +++ +++i+aviH lcl|FitnessBrowser__SB2B:6938103 3 ILVTGGAGYIGTHTVVALQQAGMEVLVLDNLSNACVEALNRVEQITgqAVPFVQGDILDKPLLMKIFMDNDIEAVIH 79 9********************************************9999**************************** PP TIGR01179 77 faaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklmvE 153 fa+l+avgEsv++Pl+YYennv++tl+L+++m++++vk+l+Fsssa+vYg++ ++pi+E++p++++npYG+sklmvE lcl|FitnessBrowser__SB2B:6938103 80 FAGLKAVGESVAQPLRYYENNVTGTLVLCQVMAEFNVKQLVFSSSATVYGDPASLPITEDFPTGATNPYGQSKLMVE 156 ***************************************************************************** PP TIGR01179 154 rilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGtcvRDyi 229 +il dl+++d++++++ LRYFn++GA+e+g iGe++++++ +l++ + +vavgkrekl+ifG+dypt+DGt+vRDyi lcl|FitnessBrowser__SB2B:6938103 157 HILADLHHSDPSWNIARLRYFNPVGAHESGLIGEDPNDIPnNLMPFISQVAVGKREKLSIFGNDYPTHDGTGVRDYI 233 ****************************************9************************************ PP TIGR01179 230 HveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaskikrelg 306 Hv Dla++Hl+ale+l ++ + +ynlG+gqg+sv+++++a++k+sgk +++e+a+rR+GD+a+++ad+ k+++elg lcl|FitnessBrowser__SB2B:6938103 234 HVVDLADGHLKALEKLRTQPGLVTYNLGTGQGYSVLDMVKAFEKASGKAVPYEIAPRRPGDIAACYADPGKATKELG 310 ***************************************************************************** PP TIGR01179 307 wkpkyddLeeiiksawdWekklkeg 331 wk+k+ ++e+ +s+w+W++ +++g lcl|FitnessBrowser__SB2B:6938103 311 WKAKLS-VDEMAASSWRWQSGNPNG 334 ******.*************99887 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: 7.52 // [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