Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate WP_011187271.1 DP_RS00115 UDP-glucose 4-epimerase GalE
Query= metacyc::BSU38860-MONOMER (339 letters) >NCBI__GCF_000025945.1:WP_011187271.1 Length = 342 Score = 467 bits (1202), Expect = e-136 Identities = 222/336 (66%), Positives = 268/336 (79%), Gaps = 2/336 (0%) Query: 3 ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62 ILVTGGAGYIGSHTC+ELL +GYE+ V+D+LSNS EAL RV+ +T K +TF++ ++LD+ Sbjct: 6 ILVTGGAGYIGSHTCLELLEAGYEVTVVDDLSNSCYEALARVETLTEKKITFHQVNVLDQ 65 Query: 63 EAVDSVFAENE--IEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120 +A+D+VF ++ AVIHFAGLKAVGESVA PL+YYHNN+TGT +LC+ M K+G+K I+ Sbjct: 66 QALDAVFVSSKKPFAAVIHFAGLKAVGESVAEPLRYYHNNVTGTLVLCDLMAKHGLKNII 125 Query: 121 FSSSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPF 180 FSSSATVYG P T PITEDFPL TNPYG+TKLM+E+IL DLH AD+EW+ LLRYFNP Sbjct: 126 FSSSATVYGDPATVPITEDFPLSCTNPYGRTKLMVEEILADLHGADHEWNACLLRYFNPV 185 Query: 181 GAHPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAE 240 GAH SGRIGEDPNGIPNNLMPY+AQVA+G+L+ LSVFGNDYPT DGTGVRDYIHVVDLA+ Sbjct: 186 GAHKSGRIGEDPNGIPNNLMPYIAQVAIGRLDYLSVFGNDYPTVDGTGVRDYIHVVDLAK 245 Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300 GHV A++K+L G YNLGTG G SVLEM AF + G +V Y+ RR GD+A A Sbjct: 246 GHVCAVKKILEGRGITTYNLGTGHGCSVLEMASAFSRACGHDVAYKIVARRAGDVAVYCA 305 Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGYK 336 D KA ELGW GLE+MC D+WRWQ +N GY+ Sbjct: 306 DATKALDELGWSTSLGLEDMCEDTWRWQKNNPTGYR 341 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: 453 Number of extensions: 13 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: 339 Length of database: 342 Length adjustment: 28 Effective length of query: 311 Effective length of database: 314 Effective search space: 97654 Effective search space used: 97654 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_011187271.1 DP_RS00115 (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.14611.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-141 456.0 0.0 3.3e-141 455.8 0.0 1.0 1 lcl|NCBI__GCF_000025945.1:WP_011187271.1 DP_RS00115 UDP-glucose 4-epimera Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_011187271.1 DP_RS00115 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.8 0.0 3.3e-141 3.3e-141 1 331 [. 5 339 .. 5 340 .. 0.98 Alignments for each domain: == domain 1 score: 455.8 bits; conditional E-value: 3.3e-141 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavle 67 +iLvtGgaGyiGsh++ +lle+g+ev v+D+ls++ eal ++e++t ++++ + ++ d+++l+av+ lcl|NCBI__GCF_000025945.1:WP_011187271.1 5 NILVTGGAGYIGSHTCLELLEAGYEVTVVDDLSNSCYEALARVETLTekKITFHQVNVLDQQALDAVFV 73 59*******************************************99999******************8 PP TIGR01179 68 ..eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpis 134 ++ + aviHfa+l+avgEsv+ePl+YY+nnv++tl+L+++m+k+g+k++iFsssa+vYg++ +vpi+ lcl|NCBI__GCF_000025945.1:WP_011187271.1 74 ssKKPFAAVIHFAGLKAVGESVAEPLRYYHNNVTGTLVLCDLMAKHGLKNIIFSSSATVYGDPATVPIT 142 557789*************************************************************** PP TIGR01179 135 EesplnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaev 202 E++pl+ +npYGr+klmvE+il dl+ ad+e++ ++LRYFn++GA+++g+iGe++++++ +l++++a+v lcl|NCBI__GCF_000025945.1:WP_011187271.1 143 EDFPLSCTNPYGRTKLMVEEILADLHGADHEWNACLLRYFNPVGAHKSGRIGEDPNGIPnNLMPYIAQV 211 ***********************************************************9********* PP TIGR01179 203 avgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieav 271 a+g+++ l++fG+dypt DGt+vRDyiHv Dla++H+ a++++ eg + ++ynlG+g+g sv+e+ +a+ lcl|NCBI__GCF_000025945.1:WP_011187271.1 212 AIGRLDYLSVFGNDYPTVDGTGVRDYIHVVDLAKGHVCAVKKILEGRGITTYNLGTGHGCSVLEMASAF 280 ********************************************************************* PP TIGR01179 272 kkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331 ++++g+d+++++ +rRaGD+a+++ada k+ +elgw+++++ Le++++++w+W+k++++g lcl|NCBI__GCF_000025945.1:WP_011187271.1 281 SRACGHDVAYKIVARRAGDVAVYCADATKALDELGWSTSLG-LEDMCEDTWRWQKNNPTG 339 *****************************************.*************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (342 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: 11.78 // [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