Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate WP_011190423.1 DP_RS16115 UDP-glucose 4-epimerase GalE
Query= metacyc::BSU38860-MONOMER (339 letters) >NCBI__GCF_000025945.1:WP_011190423.1 Length = 349 Score = 475 bits (1222), Expect = e-139 Identities = 225/335 (67%), Positives = 271/335 (80%), Gaps = 2/335 (0%) Query: 3 ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62 ILVTGGAGYIGSHTC+ELL +GYE+ V+D+LSNS EAL+RV+ +TGK +TF++ ++LD+ Sbjct: 6 ILVTGGAGYIGSHTCLELLEAGYEVTVVDDLSNSCYEALSRVEALTGKKITFHQVNVLDQ 65 Query: 63 EAVDSVFAENE--IEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIV 120 +A+D+VF ++ AVIHFAGLKAVGESVA PL YYHNN+TGT +LC+ M K+GVK I+ Sbjct: 66 QALDAVFVSSKKPFAAVIHFAGLKAVGESVAKPLHYYHNNVTGTLVLCDLMAKHGVKNII 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+ +L+ LS+FGNDYPT DGTG+RDYIHVVDLA+ Sbjct: 186 GAHKSGRIGEDPNGIPNNLMPYIAQVAIDRLDFLSIFGNDYPTVDGTGMRDYIHVVDLAK 245 Query: 241 GHVKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFA 300 GHV A++KVL G YNLGTG GYSVLEMV AF + G+++ Y+ RR GDIA C+A Sbjct: 246 GHVCAVKKVLEGQGITTYNLGTGRGYSVLEMVSAFSRTCGRDIAYKIVARRAGDIAECYA 305 Query: 301 DPAKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335 D KA EL W A GL EMC D+WRWQ +N GY Sbjct: 306 DATKALDELDWLASLGLTEMCEDTWRWQKNNPTGY 340 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: 470 Number of extensions: 15 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: 349 Length adjustment: 29 Effective length of query: 310 Effective length of database: 320 Effective search space: 99200 Effective search space used: 99200 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_011190423.1 DP_RS16115 (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.17790.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-141 456.4 0.0 2.5e-141 456.2 0.0 1.0 1 lcl|NCBI__GCF_000025945.1:WP_011190423.1 DP_RS16115 UDP-glucose 4-epimera Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_011190423.1 DP_RS16115 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.2 0.0 2.5e-141 2.5e-141 1 331 [. 5 339 .. 5 340 .. 0.99 Alignments for each domain: == domain 1 score: 456.2 bits; conditional E-value: 2.5e-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_011190423.1 5 NILVTGGAGYIGSHTCLELLEAGYEVTVVDDLSNSCYEALSRVEALTgkKITFHQVNVLDQQALDAVFV 73 59*******************************************99999******************8 PP TIGR01179 68 ..eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpis 134 ++ + aviHfa+l+avgEsv++Pl+YY+nnv++tl+L+++m+k+gvk++iFsssa+vYg++ +vpi+ lcl|NCBI__GCF_000025945.1:WP_011190423.1 74 ssKKPFAAVIHFAGLKAVGESVAKPLHYYHNNVTGTLVLCDLMAKHGVKNIIFSSSATVYGDPATVPIT 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_011190423.1 143 EDFPLSCTNPYGRTKLMVEEILADLHGADHEWNACLLRYFNPVGAHKSGRIGEDPNGIPnNLMPYIAQV 211 ***********************************************************9********* PP TIGR01179 203 avgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieav 271 a+ +++ l+ifG+dypt DGt++RDyiHv Dla++H+ a++++ eg++ ++ynlG+g+g+sv+e+++a+ lcl|NCBI__GCF_000025945.1:WP_011190423.1 212 AIDRLDFLSIFGNDYPTVDGTGMRDYIHVVDLAKGHVCAVKKVLEGQGITTYNLGTGRGYSVLEMVSAF 280 ********************************************************************* PP TIGR01179 272 kkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331 ++ +g+di++++ +rRaGD+a+++ada k+ +el+w ++++ L e+++++w+W+k++++g lcl|NCBI__GCF_000025945.1:WP_011190423.1 281 SRTCGRDIAYKIVARRAGDIAECYADATKALDELDWLASLG-LTEMCEDTWRWQKNNPTG 339 *****************************************.*************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (349 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: 10.42 // [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