Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_012971162.1 ALVIN_RS09770 UDP-glucose 4-epimerase GalE
Query= curated2:Q59745 (327 letters) >NCBI__GCF_000025485.1:WP_012971162.1 Length = 323 Score = 365 bits (937), Expect = e-106 Identities = 184/317 (58%), Positives = 218/317 (68%), Gaps = 1/317 (0%) Query: 6 VLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREFVRWGPAEEGDIRDRARLDEVLA 65 VLV GGAGYIGSHTC LA GYRP+ DN GH VRWGP E GDI DRA LD V+ Sbjct: 4 VLVTGGAGYIGSHTCKALACAGYRPITLDNLVYGHEWAVRWGPLEIGDISDRACLDAVIE 63 Query: 66 KHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFSSTCATYGL 125 +H+P A++HFAA VGESV+DP +Y NNV GTLTLL A + I VFSSTCATYG+ Sbjct: 64 RHRPEAVIHFAAYAYVGESVRDPGRYYRNNVAGTLTLLEAMRDHAIPHIVFSSTCATYGI 123 Query: 126 PQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGADFEGRIGEW 185 P P+ E H Q PINPYG +K +VE+ LAD++Q L + LRYFNAAGAD EG +GE Sbjct: 124 PDRTPITEDHPQRPINPYGASKLMVERMLADFEQAHGLGWIALRYFNAAGADPEGEVGED 183 Query: 186 HQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVRAVEYLLKG 245 H PETH IPLA+ AA GR +VFG DY T DG+C+RDYIHV DLA+AHVR++ +L G Sbjct: 184 HDPETHLIPLALQAAAGRGPQLQVFGDDYPTPDGSCIRDYIHVADLAEAHVRSLAHLRAG 243 Query: 246 GDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDKARDVLGWV 305 S A NLGTG G +V E++ A E V+ RP P RR GD L A+ DKAR +LGW Sbjct: 244 EGSGAFNLGTGQGASVLEVIAAAERVTGRPVPRAIGPRRPGDPPVLYADADKARRLLGWE 303 Query: 306 PQY-DLSEIIRSAWDWH 321 P+Y DL+E I AW WH Sbjct: 304 PRYRDLAETIEHAWKWH 320 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: 384 Number of extensions: 18 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: 323 Length adjustment: 28 Effective length of query: 299 Effective length of database: 295 Effective search space: 88205 Effective search space used: 88205 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: 48 (23.1 bits)
Align candidate WP_012971162.1 ALVIN_RS09770 (UDP-glucose 4-epimerase GalE)
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.28868.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-138 446.2 0.0 3.3e-138 446.0 0.0 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012971162.1 ALVIN_RS09770 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012971162.1 ALVIN_RS09770 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.0 0.0 3.3e-138 3.3e-138 2 327 .. 4 322 .. 3 323 .] 0.99 Alignments for each domain: == domain 1 score: 446.0 bits; conditional E-value: 3.3e-138 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 +LvtGgaGyiGsh++++l +g++ ++lDnl+ g+++a++++ l gd++d++ l+av+e+++ lcl|NCBI__GCF_000025485.1:WP_012971162.1 4 VLVTGGAGYIGSHTCKALACAGYRPITLDNLVYGHEWAVRWGP------LEIGDISDRACLDAVIERHR 66 8******************************************......999***************** PP TIGR01179 71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139 ++aviHfaa+++vgEsv++P +YY+nnv +tl+Lleam+++++ +++Fss++a+Yg ++++pi+E++p+ lcl|NCBI__GCF_000025485.1:WP_012971162.1 67 PEAVIHFAAYAYVGESVRDPGRYYRNNVAGTLTLLEAMRDHAIPHIVFSSTCATYGIPDRTPITEDHPQ 135 ********************************************************************* PP TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208 pinpYG+sklmvEr+l d+++a ++l ++LRYFn+aGAd+ege+Ge++ ++thli+l++++a+g+ + lcl|NCBI__GCF_000025485.1:WP_012971162.1 136 RPINPYGASKLMVERMLADFEQA-HGLGWIALRYFNAAGADPEGEVGEDHDPETHLIPLALQAAAGRGP 203 ***********************.********************************************* PP TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277 +l++fG+dypt+DG c+RDyiHv DlaeaH+++l l +g++s ++nlG+gqg sv+evi a+++v+g+ lcl|NCBI__GCF_000025485.1:WP_012971162.1 204 QLQVFGDDYPTPDGSCIRDYIHVADLAEAHVRSLAHLRAGEGSGAFNLGTGQGASVLEVIAAAERVTGR 272 ********************************************************************* PP TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekk 327 +++ + +rR+GDp++l+ada+k++r lgw+p+y dL+e i+ aw+W+++ lcl|NCBI__GCF_000025485.1:WP_012971162.1 273 PVPRAIGPRRPGDPPVLYADADKARRLLGWEPRYRDLAETIEHAWKWHQS 322 ***********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (323 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.15 // [ok]
This GapMind analysis is from Sep 24 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