Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate SM_b20459 SM_b20459 UDP-glucose 4-epimerase
Query= curated2:Q59745 (327 letters) >FitnessBrowser__Smeli:SM_b20459 Length = 328 Score = 342 bits (876), Expect = 1e-98 Identities = 173/318 (54%), Positives = 215/318 (67%), Gaps = 1/318 (0%) Query: 1 MAGETVLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREFVRWGPAEEGDIRDRARL 60 M +LV GGAGYIGSHT L +G PVV+DN + G+R VRWGP +GDI D RL Sbjct: 1 MVAPRILVTGGAGYIGSHTAKLLRLEGIEPVVYDNLTTGNRSAVRWGPFVQGDILDGRRL 60 Query: 61 DEVLAKHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFSSTC 120 EV+ H+P A++HFAA VGESV DP +Y NNV GTL+LL A + G++ +FSS+C Sbjct: 61 IEVIEAHQPDAVIHFAASAYVGESVADPAKYYNNNVRGTLSLLDACRQTGVDKVIFSSSC 120 Query: 121 ATYGLPQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGADFEG 180 ATYG+P +P+DE Q PINPYG+TK + E LADY +L V LRYFNA GAD EG Sbjct: 121 ATYGVPAVLPIDEATPQAPINPYGKTKLVAEHMLADYAAAFALNYVSLRYFNACGADPEG 180 Query: 181 RIGEWHQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVRAVE 240 +GEWH PETH IP A+ AA GR ++FG DY+T DGTCVRDYIHV DLA AHV A Sbjct: 181 DLGEWHDPETHLIPRALMAAAGRIPHLEIFGEDYDTPDGTCVRDYIHVADLASAHVLAYR 240 Query: 241 YLLKGGDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDKARD 300 +L KGG +VALNLGTG G ++KE+L I E++ PV + RR GD L A+ A Sbjct: 241 HLAKGGGNVALNLGTGRGFSIKEVLRTIGEITGHDVPVVFRRRRAGDPPALYADAGLACR 300 Query: 301 VLGWVPQY-DLSEIIRSA 317 LG++P+Y DL I+R+A Sbjct: 301 TLGFLPRYSDLETIVRTA 318 Lambda K H 0.319 0.137 0.415 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: 345 Number of extensions: 13 Number of successful extensions: 1 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: 327 Length of database: 328 Length adjustment: 28 Effective length of query: 299 Effective length of database: 300 Effective search space: 89700 Effective search space used: 89700 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: 48 (23.1 bits)
Align candidate SM_b20459 SM_b20459 (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.22287.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-131 422.5 0.0 5.8e-131 422.2 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SM_b20459 SM_b20459 UDP-glucose 4-epimeras Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b20459 SM_b20459 UDP-glucose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.2 0.0 5.8e-131 5.8e-131 1 321 [. 5 318 .. 5 322 .. 0.99 Alignments for each domain: == domain 1 score: 422.2 bits; conditional E-value: 5.8e-131 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidav 74 +iLvtGgaGyiGsh+++ l+ +g e vv+Dnl++g+++a++++ +v+gd+ d ++l +v+e++++dav lcl|FitnessBrowser__Smeli:SM_b20459 5 RILVTGGAGYIGSHTAKLLRLEGIEPVVYDNLTTGNRSAVRWGP------FVQGDILDGRRLIEVIEAHQPDAV 72 69******************************************......************************ PP TIGR01179 75 iHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrs 148 iHfaa+++vgEsv++P+kYY+nnv +tl+Ll+a++++gv k+iFsss+a+Yg + +pi E++p++pinpYG++ lcl|FitnessBrowser__Smeli:SM_b20459 73 IHFAASAYVGESVADPAKYYNNNVRGTLSLLDACRQTGVDKVIFSSSCATYGVPAVLPIDEATPQAPINPYGKT 146 ************************************************************************** PP TIGR01179 149 klmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDG 222 kl++E++l d++ a +l++v+LRYFn++GAd+eg++Ge + ++thli++++ +a+g+ ++leifG+dy+t+DG lcl|FitnessBrowser__Smeli:SM_b20459 147 KLVAEHMLADYAAA-FALNYVSLRYFNACGADPEGDLGEWHDPETHLIPRALMAAAGRIPHLEIFGEDYDTPDG 219 ***********999.*********************************************************** PP TIGR01179 223 tcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslva 296 tcvRDyiHv Dla+aH+ a++ l++gg+ ++nlG+g+gfs+kev++++ +++g+d++v + rRaGDp++l+a lcl|FitnessBrowser__Smeli:SM_b20459 220 TCVRDYIHVADLASAHVLAYRHLAKGGGNVALNLGTGRGFSIKEVLRTIGEITGHDVPVVFRRRRAGDPPALYA 293 ************************************************************************** PP TIGR01179 297 daskikrelgwkpkyddLeeiiksa 321 da + r+lg+ p+y dLe+i+++a lcl|FitnessBrowser__Smeli:SM_b20459 294 DAGLACRTLGFLPRYSDLETIVRTA 318 ***********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (328 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: 11.43 // [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