Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate AZOBR_RS22395 AZOBR_RS22395 UDP-glucose 4-epimerase
Query= SwissProt::Q7WTB1 (330 letters) >FitnessBrowser__azobra:AZOBR_RS22395 Length = 339 Score = 310 bits (794), Expect = 3e-89 Identities = 152/325 (46%), Positives = 210/325 (64%), Gaps = 2/325 (0%) Query: 3 VLVIGGAGYIGSHAVRELVKEGNDVLVLDALYTGHRKAVDPKAKFYQGDIEDTFLVSKIL 62 VLV GGAGY+GSH V EL+ G V+VLD L GHR AV A F + D+ D ++++ Sbjct: 7 VLVTGGAGYVGSHCVAELLDRGFRVVVLDNLRQGHRAAVPSDAAFVEADLADMDALTRVF 66 Query: 63 RDEKIDAVMHFAAYSLVPESVKKPLKYYDNNVTGMISLLQAMNDANVKYLVFSSSAATYG 122 + + DAV HFAA SLV ES++ P Y N ++L++A A V+ +VFSS+A +G Sbjct: 67 AEWRFDAVFHFAALSLVGESMRDPHLYLHGNTVNSLNLIRAATTAGVRKMVFSSTANLFG 126 Query: 123 IPKKLPITEDTPLNPINPYGETKMMMEKIMAWADKADGIKYTALRYFNVAGASSDGSIGE 182 P++ PI E+T ++P +PYGE+K +E+ + WAD+ G++ LRYFN AGA +G IGE Sbjct: 127 TPERQPIDEETTIDPGSPYGESKFFIERALHWADRCHGLRSACLRYFNAAGAHPNGIIGE 186 Query: 183 DHAPETHLIPNILKSAISGDGKFTIFGDDYDTKDGTNVRDYVQVEDLIDAHILALKHMMK 242 DH PETHLIP +L +A IFGDDY T DGT VRDYV V DL DAH+ L + Sbjct: 187 DHDPETHLIPLVLDAASGRRSHIEIFGDDYPTPDGTCVRDYVHVCDLADAHLRVLPAL-- 244 Query: 243 TNKSDVFNLGTAHGYSNLEILESAKKVTGIDIPYTMGPRRGGDPDSLVADSTKARTVLGW 302 +S FNLG GYS E++++ ++VTG+ +P +GPRR GDP L+A S + R LGW Sbjct: 245 ETRSVRFNLGNGTGYSVREVIDATERVTGLTVPVKVGPRRAGDPAMLIASSERIRGELGW 304 Query: 303 KPKHENVDDVIATAWKWHKSHPKGY 327 P+ ++D +I +AW+W + HP GY Sbjct: 305 SPRFPDLDSIIGSAWEWRRRHPGGY 329 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: 342 Number of extensions: 10 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: 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 AZOBR_RS22395 AZOBR_RS22395 (UDP-glucose 4-epimerase)
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.32455.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-126 405.2 0.0 9.7e-126 405.0 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS22395 AZOBR_RS22395 UDP-glucose 4-epim Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS22395 AZOBR_RS22395 UDP-glucose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.0 0.0 9.7e-126 9.7e-126 2 331 .. 7 328 .. 6 329 .. 0.98 Alignments for each domain: == domain 1 score: 405.0 bits; conditional E-value: 9.7e-126 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 +LvtGgaGy+Gsh v +ll++g++vvvlDnl +g++ a++ ++ve+dlad +l++v++e + lcl|FitnessBrowser__azobra:AZOBR_RS22395 7 VLVTGGAGYVGSHCVAELLDRGFRVVVLDNLRQGHRAAVPSDA-----AFVEADLADMDALTRVFAEWR 70 8***************************************998.....7******************** PP TIGR01179 71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139 +dav Hfaal vgEs+++P Y + n+vn+l+L++a ++agv+k++Fss+a ++g++e+ pi Ee+++ lcl|FitnessBrowser__azobra:AZOBR_RS22395 71 FDAVFHFAALSLVGESMRDPHLYLHGNTVNSLNLIRAATTAGVRKMVFSSTANLFGTPERQPIDEETTI 139 ********************************************************************* PP TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208 p +pYG+sk +Er l+ + + ++l+ + LRYFn+aGA+++g iGe++ ++thli+lv+++a+g+r+ lcl|FitnessBrowser__azobra:AZOBR_RS22395 140 DPGSPYGESKFFIERALHWADRC-HGLRSACLRYFNAAGAHPNGIIGEDHDPETHLIPLVLDAASGRRS 207 ********************999.********************************************* PP TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgk 277 ++eifG+dypt+DGtcvRDy+Hv+Dla+aHl+ l ale + s +nlG+g+g+sv+evi+a+++v+g lcl|FitnessBrowser__azobra:AZOBR_RS22395 208 HIEIFGDDYPTPDGTCVRDYVHVCDLADAHLRVLPALE--TRSVRFNLGNGTGYSVREVIDATERVTGL 274 *************************************9..58999************************ PP TIGR01179 278 dikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331 +++v++ +rRaGDpa+l+a++++i+ elgw+p++ dL+ ii saw+W+++++ g lcl|FitnessBrowser__azobra:AZOBR_RS22395 275 TVPVKVGPRRAGDPAMLIASSERIRGELGWSPRFPDLDSIIGSAWEWRRRHPGG 328 *************************************************99865 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.42 // [ok]
This GapMind analysis is from Sep 17 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