Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_077280163.1 B1C78_RS15970 UDP-glucose 4-epimerase GalE
Query= curated2:Q59083 (348 letters) >NCBI__GCF_002000365.1:WP_077280163.1 Length = 327 Score = 370 bits (949), Expect = e-107 Identities = 193/321 (60%), Positives = 225/321 (70%), Gaps = 1/321 (0%) Query: 11 VLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRVM 70 +LVTGGAGYIGSHV L +AG V +D+LS G REA+ VEGD G L+ RV+ Sbjct: 6 ILVTGGAGYIGSHVALMLAEAGERVVVLDNLSTGFREAVLQGT-FVEGDTGDRALVSRVL 64 Query: 71 RDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVYG 130 +H +D VMHFA +VPESV PL YYRNNT + LL C AG+ VFSSTAAVYG Sbjct: 65 AEHDIDTVMHFAAHTIVPESVSDPLKYYRNNTCATRNLLECCRDAGVRHFVFSSTAAVYG 124 Query: 131 APESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTGQ 190 P+ RED+PT PINPYG SKLM+E MLRD AA LR VILRYFNVAG+DP GR GQ Sbjct: 125 IPDDGLAREDSPTAPINPYGTSKLMSEWMLRDLSAATDLRHVILRYFNVAGSDPGGRIGQ 184 Query: 191 ATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLRR 250 +T AT LIKVAC+ LG+RP L +FGTDY TPDGT +RDYIHV+DLADAHV AL +LR Sbjct: 185 STREATLLIKVACEVALGKRPELTVFGTDYPTPDGTGVRDYIHVTDLADAHVRALAYLRD 244 Query: 251 GGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLGW 310 G S N GYG+G SVREVV +E V G +P A RRPGDPP+L+A +D IR L W Sbjct: 245 GKSSTTFNVGYGKGFSVREVVDAVERVLGTPLPVREAGRRPGDPPRLIAVSDAIRGALDW 304 Query: 311 VPKHDRLDGIVRSALSWERSL 331 P+ D LD IVR++L WER L Sbjct: 305 GPELDDLDVIVRTSLDWERRL 325 Lambda K H 0.319 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: 372 Number of extensions: 14 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: 348 Length of database: 327 Length adjustment: 28 Effective length of query: 320 Effective length of database: 299 Effective search space: 95680 Effective search space used: 95680 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 WP_077280163.1 B1C78_RS15970 (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.7204.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-138 446.8 0.0 2.1e-138 446.7 0.0 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077280163.1 B1C78_RS15970 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077280163.1 B1C78_RS15970 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.7 0.0 2.1e-138 2.1e-138 1 327 [. 5 324 .. 5 327 .] 0.99 Alignments for each domain: == domain 1 score: 446.7 bits; conditional E-value: 2.1e-138 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 +iLvtGgaGyiGshv+ l e+g +vvvlDnls+g++ea+ +++ +vegd d++ +++vl+e+ lcl|NCBI__GCF_002000365.1:WP_077280163.1 5 AILVTGGAGYIGSHVALMLAEAGERVVVLDNLSTGFREAVLQGT------FVEGDTGDRALVSRVLAEH 67 59***************************************999......******************* PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 +id+v+Hfaa + v+Esv++PlkYY+nn+ +t +Lle++++agv++++Fss+aavYg +++ E+sp lcl|NCBI__GCF_002000365.1:WP_077280163.1 68 DIDTVMHFAAHTIVPESVSDPLKYYRNNTCATRNLLECCRDAGVRHFVFSSTAAVYGIPDDGLAREDSP 136 ********************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 ++pinpYG+sklm+E++l+dl+ a ++l++viLRYFnvaG d+ g+iG+++++at lik+++eva+gkr lcl|NCBI__GCF_002000365.1:WP_077280163.1 137 TAPINPYGTSKLMSEWMLRDLSAA-TDLRHVILRYFNVAGSDPGGRIGQSTREATLLIKVACEVALGKR 204 *********************999.******************************************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 ++l++fGtdypt+DGt+vRDyiHv+Dla+aH++al +l +g+ s+++n+G+g+gfsv+ev++av++v g lcl|NCBI__GCF_002000365.1:WP_077280163.1 205 PELTVFGTDYPTPDGTGVRDYIHVTDLADAHVRALAYLRDGKSSTTFNVGYGKGFSVREVVDAVERVLG 273 ********************************************************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekk 327 ++++v++a rR+GDp++l+a ++ i+ l+w p++ddL+ i+++++dWe++ lcl|NCBI__GCF_002000365.1:WP_077280163.1 274 TPLPVREAGRRPGDPPRLIAVSDAIRGALDWGPELDDLDVIVRTSLDWERR 324 ************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (327 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.04 // [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