Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_104914353.1 C3B54_RS07945 UDP-glucose 4-epimerase GalE
Query= SwissProt::P21977 (332 letters) >NCBI__GCF_002950575.1:WP_104914353.1 Length = 324 Score = 228 bits (580), Expect = 2e-64 Identities = 137/324 (42%), Positives = 188/324 (58%), Gaps = 8/324 (2%) Query: 1 MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60 M LV GGAGYIG H V LV G E VVV+D L +G + + +G +++ + Sbjct: 1 MKFLVTGGAGYIGGHTVYSLVNAGHE-VVVIDDLSSGRAEVLPEGVVLVRGSVTNPGALD 59 Query: 61 KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120 + F + VD VIHFA + G S+EKPL +D N GM++LLE M GV +IVFSST+ Sbjct: 60 EAFSHH--VDGVIHFAGFKHAGVSVEKPLLTYDQNVVGMLRLLEAMERAGVGHIVFSSTS 117 Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180 A YG + I E P+NP +PYGESKL+ E I++ A G+K+ LRYFNV G+ V Sbjct: 118 AVYGDVDAPVIHEDAPKNPASPYGESKLVGEWILRDQGVATGLKHCSLRYFNVVGSG--V 175 Query: 181 RLVRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVEY 240 + S LL ++ A G E +FG DY+TPDGT +RDY+H LADAH+ E Sbjct: 176 PGIYDTSPYSLLSMVF-AALGRGETPGVFGTDYDTPDGTCIRDYIHVQALADAHVQVAEK 234 Query: 241 LRKGNE-STAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKART 299 L G A+NLGS TG S Q++ +VTG + E RR GDP ++AS E A Sbjct: 235 LVSGQPLQGAYNLGSGTGSSVAQMMTEVARVTGIDFEPEAWPRRAGDPMKVVASGEAAAR 294 Query: 300 VLGWKPQFDNIEKIIASAWAWHSS 323 +GW Q ++ ++++SAW +S+ Sbjct: 295 DVGWTMQ-QSVAEMVSSAWREYSA 317 Lambda K H 0.318 0.136 0.401 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: 323 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 332 Length of database: 324 Length adjustment: 28 Effective length of query: 304 Effective length of database: 296 Effective search space: 89984 Effective search space used: 89984 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_104914353.1 C3B54_RS07945 (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.2036129.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-99 318.0 0.0 3.4e-99 317.8 0.0 1.0 1 NCBI__GCF_002950575.1:WP_104914353.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002950575.1:WP_104914353.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 317.8 0.0 3.4e-99 3.4e-99 2 323 .. 3 313 .. 2 320 .. 0.94 Alignments for each domain: == domain 1 score: 317.8 bits; conditional E-value: 3.4e-99 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 LvtGgaGyiG h+v +l ++g+evvv+D+ls+g +e+l+++ +lv+g +++ +l+++++ +++d v NCBI__GCF_002950575.1:WP_104914353.1 3 FLVTGGAGYIGGHTVYSLVNAGHEVVVIDDLSSGRAEVLPEGV-----VLVRGSVTNPGALDEAFS-HHVDGV 69 79**************************************998.....8****************7.679*** PP TIGR01179 75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147 iHfa++++ g sv++Pl Y++nvv+ l+Lleam++agv +++Fss++avYg+ ++ +i+E++p np++pYG+ NCBI__GCF_002950575.1:WP_104914353.1 70 IHFAGFKHAGVSVEKPLLTYDQNVVGMLRLLEAMERAGVGHIVFSSTSAVYGDVDAPVIHEDAPKNPASPYGE 142 ************************************************************************* PP TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGtdypt 219 skl+ E+il+d a ++lk+++LRYFnv+G g + + + l+ + + +a+g+ e+ +fGtdy+t NCBI__GCF_002950575.1:WP_104914353.1 143 SKLVGEWILRDQGVA-TGLKHCSLRYFNVVGSGVPGI----YDTSPySLLSM-VFAALGRGETPGVFGTDYDT 209 ************999.***************876653....44555266665.5689**************** PP TIGR01179 220 kDGtcvRDyiHveDlaeaHlaalealeegge.sevynlGagqgfsvkevieavkkvsgkdikveladrRaGDp 291 +DGtc+RDyiHv+ la+aH++ e+l +g+ + +ynlG+g+g sv +++ +v +v+g d++ e +rRaGDp NCBI__GCF_002950575.1:WP_104914353.1 210 PDGTCIRDYIHVQALADAHVQVAEKLVSGQPlQGAYNLGSGTGSSVAQMMTEVARVTGIDFEPEAWPRRAGDP 282 **************************999652679************************************** PP TIGR01179 292 aslvadaskikrelgwkpkyddLeeiiksawd 323 ++va+ + + r +gw+ + ++e+++saw+ NCBI__GCF_002950575.1:WP_104914353.1 283 MKVVASGEAAARDVGWTMQQS-VAEMVSSAWR 313 ******************999.*********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (324 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: 00:00:00.00 # Mc/sec: 13.04 // [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