Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_040660816.1 ON16_RS07550 UDP-glucose 4-epimerase GalE
Query= SwissProt::P21977 (332 letters) >NCBI__GCF_000307265.1:WP_040660816.1 Length = 329 Score = 359 bits (922), Expect = e-104 Identities = 189/331 (57%), Positives = 230/331 (69%), Gaps = 3/331 (0%) Query: 1 MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60 M+ILVLGGAGYIGSH LV G++ VVV D+L TG R AV A FY+GD+ D+ F Sbjct: 1 MSILVLGGAGYIGSHTALALVNAGRD-VVVADNLETGFRKAVPEMARFYKGDIRDRAFCD 59 Query: 61 KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120 +F E +D VIHFAA S VGESM PLKY+ NN G LLE M GV IVFSSTA Sbjct: 60 GLF-EREQIDGVIHFAANSQVGESMTNPLKYYANNMGGTRVLLESMVAHGVGKIVFSSTA 118 Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180 ATYG PE +PILET P N YGE+KL ME +MKW A+G++YV LRYFN GA Sbjct: 119 ATYGEPERVPILETDATVPTNCYGETKLSMEKMMKWISVAHGLRYVALRYFNACGAQPDG 178 Query: 181 RLVRTRS-ETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVE 239 + + ETHL+P+ILQV G REKI IFGDDY TPDGT +RDY+H DLA AH+LA++ Sbjct: 179 SIGEAHNPETHLIPVILQVPGGQREKISIFGDDYPTPDGTCIRDYIHVCDLAQAHILALD 238 Query: 240 YLRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKART 299 YL E+ FNLG+ GFS +++E ARKVTG IP E RR GDP LIASSEKA+T Sbjct: 239 YLLSSGENNVFNLGNGVGFSVKEVIEEARKVTGHAIPTEVLPRRAGDPAQLIASSEKAKT 298 Query: 300 VLGWKPQFDNIEKIIASAWAWHSSHPKGYDD 330 +LGWKP+F+++ II +AW WH +HP+G++D Sbjct: 299 LLGWKPEFEDLHTIIQTAWDWHKTHPRGFED 329 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: 353 Number of extensions: 14 Number of successful extensions: 4 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: 329 Length adjustment: 28 Effective length of query: 304 Effective length of database: 301 Effective search space: 91504 Effective search space used: 91504 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_040660816.1 ON16_RS07550 (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.76678.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-138 445.3 0.0 6.2e-138 445.1 0.0 1.0 1 NCBI__GCF_000307265.1:WP_040660816.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000307265.1:WP_040660816.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.1 0.0 6.2e-138 6.2e-138 2 330 .. 3 325 .. 2 327 .. 0.99 Alignments for each domain: == domain 1 score: 445.1 bits; conditional E-value: 6.2e-138 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 iLv GgaGyiGsh++ +l ++g +vvv Dnl +g+++a++++ +++gd++d++ + ++e+e+id v NCBI__GCF_000307265.1:WP_040660816.1 3 ILVLGGAGYIGSHTALALVNAGRDVVVADNLETGFRKAVPEMA-----RFYKGDIRDRAFCDGLFEREQIDGV 70 9*****************************************9.....5************************ PP TIGR01179 75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGr 147 iHfaa +vgEs+++PlkYY+nn+ +t +Lle+m+++gv k++Fss+aa+Yge+e+vpi E+ ++ p+n YG+ NCBI__GCF_000307265.1:WP_040660816.1 71 IHFAANSQVGESMTNPLKYYANNMGGTRVLLESMVAHGVGKIVFSSTAATYGEPERVPILETDATVPTNCYGE 143 ************************************************************************* PP TIGR01179 148 sklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptk 220 +kl +E+++k ++ a ++l++v+LRYFn++GA+++g+iGea++++thli+++++v g+rek++ifG+dypt+ NCBI__GCF_000307265.1:WP_040660816.1 144 TKLSMEKMMKWISVA-HGLRYVALRYFNACGAQPDGSIGEAHNPETHLIPVILQVPGGQREKISIFGDDYPTP 215 ************999.********************************************************* PP TIGR01179 221 DGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpas 293 DGtc+RDyiHv+Dla+aH+ al++l ++ge +v+nlG+g gfsvkevie+++kv+g+ i++e+ +rRaGDpa+ NCBI__GCF_000307265.1:WP_040660816.1 216 DGTCIRDYIHVCDLAQAHILALDYLLSSGENNVFNLGNGVGFSVKEVIEEARKVTGHAIPTEVLPRRAGDPAQ 288 ************************************************************************* PP TIGR01179 294 lvadaskikrelgwkpkyddLeeiiksawdWekklke 330 l+a+++k+k+ lgwkp+++dL++ii++awdW+k++++ NCBI__GCF_000307265.1:WP_040660816.1 289 LIASSEKAKTLLGWKPEFEDLHTIIQTAWDWHKTHPR 325 *********************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (329 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: 25.50 // [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