Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_010961676.1 MCA_RS12025 UDP-glucose 4-epimerase GalE
Query= curated2:Q59083 (348 letters) >NCBI__GCF_000008325.1:WP_010961676.1 Length = 341 Score = 370 bits (951), Expect = e-107 Identities = 188/321 (58%), Positives = 229/321 (71%), Gaps = 1/321 (0%) Query: 11 VLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRVM 70 +LVTGGAGYIGSHV+ L +AG V +D+LS G R+A+ +EGD G LLD++M Sbjct: 6 ILVTGGAGYIGSHVVKTLGEAGERLVVLDNLSTGFRDAVLYG-DFIEGDTGDDVLLDKIM 64 Query: 71 RDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVYG 130 RD+ V+AVMHFA +VPESV PL YY NNT + TLL +C +AG+ +FSSTAAVYG Sbjct: 65 RDYEVEAVMHFAAHTIVPESVENPLKYYGNNTCKTRTLLESCRKAGVSHFIFSSTAAVYG 124 Query: 131 APESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTGQ 190 PE E +P PINPYG+SKLM+E MLRD A LR V+LRYFNVAG+DP GR GQ Sbjct: 125 IPEGEFALETSPLAPINPYGSSKLMSEIMLRDLSTASPLRHVVLRYFNVAGSDPEGRIGQ 184 Query: 191 ATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLRR 250 +T AT LIKVA + G+R L IFGTDY TPDGT IRDYIHVSDLADAHV AL +LR Sbjct: 185 STAKATLLIKVAAEVATGKRDRLCIFGTDYPTPDGTGIRDYIHVSDLADAHVAALAYLRA 244 Query: 251 GGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLGW 310 GG S +NCGYG G SVRE++ T+ V+G + RRPGDPP+LVAG +RIRE L W Sbjct: 245 GGESRTLNCGYGHGYSVREIIDTMNRVNGTPIAVEERPRRPGDPPRLVAGVERIREILEW 304 Query: 311 VPKHDRLDGIVRSALSWERSL 331 P++D ++ IVR++L WER L Sbjct: 305 TPRYDDIELIVRTSLEWERKL 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: 410 Number of extensions: 12 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: 341 Length adjustment: 29 Effective length of query: 319 Effective length of database: 312 Effective search space: 99528 Effective search space used: 99528 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_010961676.1 MCA_RS12025 (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.5285.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-136 439.1 0.0 4.8e-136 438.9 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961676.1 MCA_RS12025 UDP-glucose 4-epimer Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010961676.1 MCA_RS12025 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.9 0.0 4.8e-136 4.8e-136 2 328 .. 6 325 .. 5 329 .. 0.99 Alignments for each domain: == domain 1 score: 438.9 bits; conditional E-value: 4.8e-136 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 iLvtGgaGyiGshvv++l e+g ++vvlDnls+g+++a+ +++ ++egd d l++++++ + lcl|NCBI__GCF_000008325.1:WP_010961676.1 6 ILVTGGAGYIGSHVVKTLGEAGERLVVLDNLSTGFRDAVLYGD------FIEGDTGDDVLLDKIMRDYE 68 9******************************************......******************** PP TIGR01179 71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139 ++av+Hfaa + v+Esv++PlkYY nn+ t +Lle+++kagv ++iFss+aavYg +e E+spl lcl|NCBI__GCF_000008325.1:WP_010961676.1 69 VEAVMHFAAHTIVPESVENPLKYYGNNTCKTRTLLESCRKAGVSHFIFSSTAAVYGIPEGEFALETSPL 137 ********************************************************************* PP TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208 +pinpYG sklm+E +l+dl++a + l++v+LRYFnvaG d+eg+iG+++ +at lik++aeva+gkr+ lcl|NCBI__GCF_000008325.1:WP_010961676.1 138 APINPYGSSKLMSEIMLRDLSTA-SPLRHVVLRYFNVAGSDPEGRIGQSTAKATLLIKVAAEVATGKRD 205 ***********************.9******************************************** PP TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277 +l ifGtdypt+DGt++RDyiHv+Dla+aH+aal +l +gges+++n+G+g+g+sv+e+i+++++v g+ lcl|NCBI__GCF_000008325.1:WP_010961676.1 206 RLCIFGTDYPTPDGTGIRDYIHVSDLADAHVAALAYLRAGGESRTLNCGYGHGYSVREIIDTMNRVNGT 274 ********************************************************************* PP TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328 +i+ve+ +rR+GDp++lva ++i++ l+w+p+ydd+e i++++++We+kl lcl|NCBI__GCF_000008325.1:WP_010961676.1 275 PIAVEERPRRPGDPPRLVAGVERIREILEWTPRYDDIELIVRTSLEWERKL 325 ************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (341 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: 12.12 // [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