Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_013136369.1 ARNIT_RS12860 UDP-glucose 4-epimerase GalE
Query= SwissProt::Q7WTB1 (330 letters) >NCBI__GCF_000092245.1:WP_013136369.1 Length = 339 Score = 267 bits (683), Expect = 2e-76 Identities = 143/329 (43%), Positives = 207/329 (62%), Gaps = 11/329 (3%) Query: 1 MKVLVIGGAGYIGSHAVRELVKEGN-DVLVLDALYTGHRKAVDPKA-----KFYQGDIED 54 M +L+ GGAGYIGSH ++L++ ++ +LD L TG K +D KF + D+++ Sbjct: 1 MNILITGGAGYIGSHVAKQLLETTTYNITILDNLSTGSAKTLDTLKTIRDFKFIELDLKE 60 Query: 55 TFLVSKILRDEKIDAVMHFAAYSLVPESVKKPLKYYDNNVTGMISLLQAMNDANVKYLVF 114 V+ L+++KI+ ++HFAA +VPESV+ PLKYY NN +L++ + NV +F Sbjct: 61 FDKVNSALKEKKINTIIHFAASIVVPESVENPLKYYMNNTVNTTNLIKRAVENNVSKFIF 120 Query: 115 SSSAATYGIPKKLPIT---EDTPLNPINPYGETKMMMEKIMA-WADKADGIKYTALRYFN 170 SS+AA YG P +P T E P NPINPYG +K+M EK++ A KY RYFN Sbjct: 121 SSTAAVYGEPTNIPNTGVDESYPTNPINPYGMSKLMSEKVLQDTASVNSDFKYVIFRYFN 180 Query: 171 VAGASSDGSIGEDHAPETHLIPNILKSAISGDGKFTIFGDDYDTKDGTNVRDYVQVEDLI 230 VAGAS+D +IGE H PETHLIP + K+A+ K I+GDDY TKDG+N+RDYV V DL Sbjct: 181 VAGASADLTIGECHEPETHLIPLVAKTALGKRDKILIYGDDYPTKDGSNLRDYVHVLDLA 240 Query: 231 DAHILALKHMMKTNKSDVFNLGTAHGYSNLEILESAKKVTGIDIPYTMGPRRGGDPDSLV 290 DAHI A+ + N S++FN G G+S E++++ K VT + + RR GDP LV Sbjct: 241 DAHIKAI-DFLNENSSNIFNCGYGKGFSVKEVVKTMKLVTNTNFISEIVSRRAGDPAILV 299 Query: 291 ADSTKARTVLGWKPKHENVDDVIATAWKW 319 +D+ K ++ + W PK+E++ + +A+ W Sbjct: 300 SDNRKIKSKMNWIPKYEDLPLICKSAYDW 328 Lambda K H 0.315 0.134 0.395 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: 334 Number of extensions: 17 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: 330 Length of database: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_013136369.1 ARNIT_RS12860 (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.8583.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-138 445.4 0.2 5.7e-138 445.2 0.2 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013136369.1 ARNIT_RS12860 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013136369.1 ARNIT_RS12860 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.2 0.2 5.7e-138 5.7e-138 1 328 [. 2 332 .. 2 336 .. 0.97 Alignments for each domain: == domain 1 score: 445.2 bits; conditional E-value: 5.7e-138 TIGR01179 1 kiLvtGgaGyiGshvvrqllek.gkevvvlDnlskgskealkalekitevklvegdladkekleavlee 68 +iL+tGgaGyiGshv++qlle+ ++++ +lDnls+gs+++l +l++i+++k++e dl++ k++++l+e lcl|NCBI__GCF_000092245.1:WP_013136369.1 2 NILITGGAGYIGSHVAKQLLETtTYNITILDNLSTGSAKTLDTLKTIRDFKFIELDLKEFDKVNSALKE 70 59****************99862578******************************************* PP TIGR01179 69 ekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvp...is 134 +ki+++iHfaa+i v+Esv++PlkYY+nn+vnt++L++ ++ +v k+iFss+aavYge++++p + lcl|NCBI__GCF_000092245.1:WP_013136369.1 71 KKINTIIHFAASIVVPESVENPLKYYMNNTVNTTNLIKRAVENNVSKFIFSSTAAVYGEPTNIPntgVD 139 *************************************************************99855578 PP TIGR01179 135 EesplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaeva 203 E+ p+npinpYG sklm+E++l+d++++++++k+vi RYFnvaGA+ + +iGe ++++thli+lva++a lcl|NCBI__GCF_000092245.1:WP_013136369.1 140 ESYPTNPINPYGMSKLMSEKVLQDTASVNSDFKYVIFRYFNVAGASADLTIGECHEPETHLIPLVAKTA 208 ********************************************************************* PP TIGR01179 204 vgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavk 272 +gkr+k+ i+G+dyptkDG +RDy+Hv Dla+aH++a++ l+e + s+++n+G+g+gfsvkev++++k lcl|NCBI__GCF_000092245.1:WP_013136369.1 209 LGKRDKILIYGDDYPTKDGSNLRDYVHVLDLADAHIKAIDFLNE-NSSNIFNCGYGKGFSVKEVVKTMK 276 *****************************************996.99********************** PP TIGR01179 273 kvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekkl 328 v+++++ e+ rRaGDpa lv+d+ kik++++w pky+dL i+ksa+dWe++l lcl|NCBI__GCF_000092245.1:WP_013136369.1 277 LVTNTNFISEIVSRRAGDPAILVSDNRKIKSKMNWIPKYEDLPLICKSAYDWENRL 332 *****************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (339 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: 00:00:00.01 # Mc/sec: 7.53 // [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