Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_067471624.1 BJL86_RS07645 UDP-glucose 4-epimerase GalE
Query= SwissProt::P21977 (332 letters) >NCBI__GCF_001659785.1:WP_067471624.1 Length = 325 Score = 292 bits (747), Expect = 9e-84 Identities = 166/332 (50%), Positives = 212/332 (63%), Gaps = 16/332 (4%) Query: 1 MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60 M +LV GGAGY+GS L+ +G E VVV+D L TG+R V P+A F +GDL D R Sbjct: 1 MRVLVTGGAGYVGSCCAAELISRGHE-VVVLDDLSTGNRDGVPPEATFIEGDLIS-DSAR 58 Query: 61 KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120 + VDAVIH AA SLVGES+E+P +Y+ N + LL+ M E VK IVFSSTA Sbjct: 59 AL----EGVDAVIHCAARSLVGESVEQPAEYWHGNVVSTLALLDAMREADVKNIVFSSTA 114 Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180 ATYG PE++PI E P P N YG +KL ++ + AYG LRYFNVAGA+L Sbjct: 115 ATYGEPEQVPITEDMPTRPTNTYGATKLAIDMAITSYCVAYGFAATSLRYFNVAGAHLGF 174 Query: 181 RLVRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVEY 240 R ETHL+P++LQVA G REKI +FGDD+ T DGT RDY+H DLADAH+LA+E Sbjct: 175 GENRV-VETHLIPLVLQVAAGHREKIFVFGDDWPTTDGTCARDYIHVGDLADAHVLALES 233 Query: 241 LRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKARTV 300 G E FNLGS GFS Q+++ R VTG EIPA+ + RR GDP L+ASSE+A++V Sbjct: 234 NAAG-EHRIFNLGSGEGFSVQQVIDVCRTVTGHEIPAQVSPRRAGDPATLVASSEQAKSV 292 Query: 301 LGWKPQFDNIEKIIASAWAW--------HSSH 324 LGW+P ++ ++ AW + HS+H Sbjct: 293 LGWQPSRTDLTTVVEDAWEFLRALGDRAHSAH 324 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: 289 Number of extensions: 9 Number of successful extensions: 5 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: 332 Length of database: 325 Length adjustment: 28 Effective length of query: 304 Effective length of database: 297 Effective search space: 90288 Effective search space used: 90288 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_067471624.1 BJL86_RS07645 (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.3432728.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-116 373.5 0.0 4.6e-116 373.2 0.0 1.0 1 NCBI__GCF_001659785.1:WP_067471624.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001659785.1:WP_067471624.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.2 0.0 4.6e-116 4.6e-116 1 325 [. 2 313 .. 2 319 .. 0.96 Alignments for each domain: == domain 1 score: 373.2 bits; conditional E-value: 4.6e-116 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekida 73 ++LvtGgaGy+Gs + +l ++g+evvvlD+ls+g+++ ++ + +++egdl ++ + + e +da NCBI__GCF_001659785.1:WP_067471624.1 2 RVLVTGGAGYVGSCCAAELISRGHEVVVLDDLSTGNRDGVPPEA-----TFIEGDLISDSA--R--ALEGVDA 65 69***************************************998.....7*****976542..3..34689** PP TIGR01179 74 viHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYG 146 viH aa+ vgEsv++P++Y++ nvv+tl Ll+am++a vk+++Fss+aa+Yge+e+vpi+E++p+ p+n YG NCBI__GCF_001659785.1:WP_067471624.1 66 VIHCAARSLVGESVEQPAEYWHGNVVSTLALLDAMREADVKNIVFSSTAATYGEPEQVPITEDMPTRPTNTYG 138 ************************************************************************* PP TIGR01179 147 rsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdypt 219 ++kl+++ ++ + a +++ ++LRYFnvaGA+ Ge+ +thli+lv++va+g+rek+ +fG+d+pt NCBI__GCF_001659785.1:WP_067471624.1 139 ATKLAIDMAITSYCVA-YGFAATSLRYFNVAGAHLG--FGENRVVETHLIPLVLQVAAGHREKIFVFGDDWPT 208 *************999.****************985..8********************************** PP TIGR01179 220 kDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpa 292 +DGtc RDyiHv Dla+aH+ ale ++ ge +++nlG+g+gfsv++vi+ +++v+g++i++++++rRaGDpa NCBI__GCF_001659785.1:WP_067471624.1 209 TDGTCARDYIHVGDLADAHVLALESNAA-GEHRIFNLGSGEGFSVQQVIDVCRTVTGHEIPAQVSPRRAGDPA 280 ************************9885.899***************************************** PP TIGR01179 293 slvadaskikrelgwkpkyddLeeiiksawdWe 325 +lva+++++k++lgw+p+++dL +++++aw++ NCBI__GCF_001659785.1:WP_067471624.1 281 TLVASSEQAKSVLGWQPSRTDLTTVVEDAWEFL 313 ******************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (325 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: 24.90 // [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