Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate 350151 BT0623 putative UDP-glucose 4-epimerase (NCBI ptt file)
Query= uniprot:L0FXG3 (337 letters) >FitnessBrowser__Btheta:350151 Length = 344 Score = 399 bits (1024), Expect = e-116 Identities = 196/338 (57%), Positives = 256/338 (75%), Gaps = 2/338 (0%) Query: 2 QQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDCN 61 ++IL+TGG GYIGSHT V L N+GYE II+DN SNS+ +V++ +EK+ G + + DC Sbjct: 3 ERILVTGGTGYIGSHTVVELQNSGYEVIIIDNLSNSSADVVDNIEKVSGIRPAFEKLDCL 62 Query: 62 DRKFMQAVFEE-NDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDI 120 D + AVF + ++ +IHFAASKAVGES + PL YY NN+ SLI LLE M + GV+ I Sbjct: 63 DFAGLDAVFAKYKGIKAIIHFAASKAVGESVEKPLLYYRNNLVSLINLLELMPKHGVEGI 122 Query: 121 VFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYFN 180 VFSSSCTVYGQPD+LPV E P K AESPYGNTK+I E+I+ D + SGAP + LRYFN Sbjct: 123 VFSSSCTVYGQPDELPVTEKAPIKKAESPYGNTKQINEEIIRDTIASGAPINAILLRYFN 182 Query: 181 PIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDL 240 PIGAHP++L+GELP GVP NLIP++TQT GIREK++VFGDDY+TPDG+CIRD+I+V+DL Sbjct: 183 PIGAHPTALLGELPNGVPQNLIPYLTQTAMGIREKLSVFGDDYDTPDGSCIRDFINVVDL 242 Query: 241 ADAHVKSIQYLADQPE-NFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDI 299 A AHV +I+ + +Q + +++FN+GTG G +V+E+I FEK + LNY+I RR+GDI Sbjct: 243 AKAHVIAIRRILEQKQKEKVEVFNIGTGRGVSVLELINGFEKATGVKLNYQIVGRRAGDI 302 Query: 300 EKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK 337 EKVWAN D ++ LGW LE+ LR AWNWQL L++ Sbjct: 303 EKVWANPDYANQELGWKAVETLEDTLRSAWNWQLKLRE 340 Lambda K H 0.316 0.136 0.403 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: 413 Number of extensions: 12 Number of successful extensions: 3 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: 337 Length of database: 344 Length adjustment: 28 Effective length of query: 309 Effective length of database: 316 Effective search space: 97644 Effective search space used: 97644 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 350151 BT0623 (putative UDP-glucose 4-epimerase (NCBI ptt file))
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.25000.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-124 400.0 0.0 3.6e-124 399.9 0.0 1.0 1 lcl|FitnessBrowser__Btheta:350151 BT0623 putative UDP-glucose 4-ep Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350151 BT0623 putative UDP-glucose 4-epimerase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.9 0.0 3.6e-124 3.6e-124 1 329 [. 4 339 .. 4 342 .. 0.96 Alignments for each domain: == domain 1 score: 399.9 bits; conditional E-value: 3.6e-124 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeek.ida 73 +iLvtGg+GyiGsh+v++l+++g+ev+++Dnls++s++++ ++ek++ + ++ + d d + l+av+++ k i+a lcl|FitnessBrowser__Btheta:350151 4 RILVTGGTGYIGSHTVVELQNSGYEVIIIDNLSNSSADVVDNIEKVSgiRPAFEKLDCLDFAGLDAVFAKYKgIKA 79 69********************************************999999****************986559** PP TIGR01179 74 viHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pinpYGrs 148 +iHfaa++avgEsv++Pl YY+nn+v+ ++Lle+m k+gv+ ++Fsss++vYg+++++p++E++p++ +++pYG++ lcl|FitnessBrowser__Btheta:350151 80 IIHFAASKAVGESVEKPLLYYRNNLVSLINLLELMPKHGVEGIVFSSSCTVYGQPDELPVTEKAPIKkAESPYGNT 155 *****************************************************************9989******* PP TIGR01179 149 klmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdyptkDGt 223 k + E+i++d+ + + ++ ++LRYFn++GA++ +Ge +++ + +li++++++a+g rekl++fG+dy+t+DG lcl|FitnessBrowser__Btheta:350151 156 KQINEEIIRDTIASGAPINAILLRYFNPIGAHPTALLGELPNGVPqNLIPYLTQTAMGIREKLSVFGDDYDTPDGS 231 **************************************************************************** PP TIGR01179 224 cvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslva 296 c+RD+i v Dla+aH+ a++ + e+ +++ev+n+G+g+g sv+e+i+ ++k++g+++++++ rRaGD+ +++a lcl|FitnessBrowser__Btheta:350151 232 CIRDFINVVDLAKAHVIAIRRILEQkqkEKVEVFNIGTGRGVSVLELINGFEKATGVKLNYQIVGRRAGDIEKVWA 307 *******************9765432227899******************************************** PP TIGR01179 297 daskikrelgwkpkyddLeeiiksawdWekklk 329 +++++++elgwk+ + Le+ ++saw+W+ kl+ lcl|FitnessBrowser__Btheta:350151 308 NPDYANQELGWKAVET-LEDTLRSAWNWQLKLR 339 ************9988.***********98865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (344 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.84 // [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