Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate Synpcc7942_0320 Synpcc7942_0320 UDP-galactose 4-epimerase
Query= curated2:Q59745 (327 letters) >FitnessBrowser__SynE:Synpcc7942_0320 Length = 332 Score = 369 bits (946), Expect = e-107 Identities = 184/330 (55%), Positives = 228/330 (69%), Gaps = 4/330 (1%) Query: 1 MAGETVLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREF---VRWGPAEEGDIRDR 57 +AG T+LV GGAGYIGSHT L +GY+P+V DN SNG R V P GD RDR Sbjct: 1 VAGATILVTGGAGYIGSHTVRALQAQGYQPIVLDNLSNGQRAIAAEVLQVPLIVGDTRDR 60 Query: 58 ARLDEVLAKHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFS 117 LD + A+H A++HFAA IEVGESV+DP +FY NNV G+LTLL A AAG VFS Sbjct: 61 LLLDRLFAEHPIQAVIHFAASIEVGESVRDPGNFYANNVSGSLTLLQAMVAAGCQQLVFS 120 Query: 118 STCATYGLPQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGAD 177 STCATYGLPQ +P+ E H Q PINPYGR+K++VEQ L D+ LRSV+ RYFNAAGAD Sbjct: 121 STCATYGLPQVIPIPEDHPQAPINPYGRSKWMVEQFLQDFQAAYGLRSVIFRYFNAAGAD 180 Query: 178 FEGRIGEWHQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVR 237 +G +GE H PETH IPL + AA G+R +V+G+DY T DGTC+RDYIHV DLADAHVR Sbjct: 181 PKGDLGEAHDPETHLIPLVLQAAAGQRPSIQVYGTDYPTSDGTCIRDYIHVCDLADAHVR 240 Query: 238 AVEYLLKGGDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDK 297 + YL GG + A NLG G G +VKE++ E V+ R PV+ RR GD+ LV ++DK Sbjct: 241 GLTYLADGGATTAFNLGNGNGFSVKEVIATAERVTQRSIPVQLSDRRPGDAIALVGSSDK 300 Query: 298 ARDVLGWVPQY-DLSEIIRSAWDWHAKSNQ 326 AR +LGW PQ+ L +I+ AW W + ++ Sbjct: 301 ARQILGWEPQFPSLETMIQHAWQWQQRCDR 330 Lambda K H 0.319 0.137 0.415 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: 367 Number of extensions: 19 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: 327 Length of database: 332 Length adjustment: 28 Effective length of query: 299 Effective length of database: 304 Effective search space: 90896 Effective search space used: 90896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate Synpcc7942_0320 Synpcc7942_0320 (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.17319.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-140 453.3 0.0 2.2e-140 453.2 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0320 Synpcc7942_0320 UDP-galactose 4- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0320 Synpcc7942_0320 UDP-galactose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.2 0.0 2.2e-140 2.2e-140 2 329 .. 6 329 .. 5 332 .] 0.98 Alignments for each domain: == domain 1 score: 453.2 bits; conditional E-value: 2.2e-140 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 iLvtGgaGyiGsh+vr+l+++g++ +vlDnls+g++ + ++ +v l+ gd +d+ l+++++e+ lcl|FitnessBrowser__SynE:Synpcc7942_0320 6 ILVTGGAGYIGSHTVRALQAQGYQPIVLDNLSNGQRAIAAEVL---QVPLIVGDTRDRLLLDRLFAEHP 71 9*********************************998776665...7********************** PP TIGR01179 71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139 i+aviHfaa+i+vgEsv++P ++Y+nnv+++l+Ll+am++ag+++l+Fss++a+Yg ++ +pi E++p+ lcl|FitnessBrowser__SynE:Synpcc7942_0320 72 IQAVIHFAASIEVGESVRDPGNFYANNVSGSLTLLQAMVAAGCQQLVFSSTCATYGLPQVIPIPEDHPQ 140 ********************************************************************* PP TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208 +pinpYGrsk mvE+ l+d++ a ++l+ vi RYFn+aGAd++g++Gea+ ++thli+lv+++a+g+r+ lcl|FitnessBrowser__SynE:Synpcc7942_0320 141 APINPYGRSKWMVEQFLQDFQAA-YGLRSVIFRYFNAAGADPKGDLGEAHDPETHLIPLVLQAAAGQRP 208 ********************999.********************************************* PP TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277 +++++Gtdypt+DGtc+RDyiHv+Dla+aH++ l +l++gg ++++nlG+g+gfsvkevi ++++v+ + lcl|FitnessBrowser__SynE:Synpcc7942_0320 209 SIQVYGTDYPTSDGTCIRDYIHVCDLADAHVRGLTYLADGGATTAFNLGNGNGFSVKEVIATAERVTQR 277 ********************************************************************* PP TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329 +i+v+l+drR+GD +lv++++k+++ lgw+p++ Le++i+ aw+W++++ lcl|FitnessBrowser__SynE:Synpcc7942_0320 278 SIPVQLSDRRPGDAIALVGSSDKARQILGWEPQFPSLETMIQHAWQWQQRCD 329 *************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (332 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.10 // [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