Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate PP_3129 PP_3129 UDP-glucose 4-epimerase
Query= curated2:Q9KDV3 (334 letters) >FitnessBrowser__Putida:PP_3129 Length = 321 Score = 323 bits (827), Expect = 5e-93 Identities = 162/323 (50%), Positives = 210/323 (65%), Gaps = 5/323 (1%) Query: 1 MAILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALSDVTFYHGDIRDDQLLDTI 60 M LV GGAGYIGSH V LL G +V+V D + G + + DI D+ LD + Sbjct: 1 MKYLVVGGAGYIGSHMVKHLLAAGHEVLVADLVSPGPG-----IQWAKLDIADEAALDVL 55 Query: 61 FTTHSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAATY 120 F D V HFA+ VGESV P +YY+NNV T +LL+ M+ ++ +VFSS+AA Y Sbjct: 56 FGVCRFDAVFHFASFIQVGESVSAPGKYYQNNVAATLSLLQAMVNAGIRHLVFSSSAAVY 115 Query: 121 GEPVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGRIG 180 G P +PI E+ P NPYG +K +E++ AYGL+ V LRYFNAAGADP G++G Sbjct: 116 GNPQYVPIDEAHTKGPINPYGLSKWMVEQILEDFDRAYGLKSVSLRYFNAAGADPEGQLG 175 Query: 181 EDHSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEHLR 240 E H PE+HLIP++LQ A G+RE V +FG DY T DG+CIRDY+HV DLA AH LA ++L Sbjct: 176 ERHEPETHLIPLILQAASGRREAVTVFGRDYDTPDGTCIRDYVHVADLAAAHALAVDYLL 235 Query: 241 KDGQSGSFNLGNGKGFSVKEVIEVCRQVTGHPIPAEIAPRRSGDPASLIASSEKAQTILG 300 G+ +FNLGNG GFSV++VI+ R VTG I A A RR+GDP L+A + KA +LG Sbjct: 236 DGGERAAFNLGNGLGFSVQQVIDTARAVTGRQITALDAQRRAGDPPRLVADASKAMQVLG 295 Query: 301 WEPKYPSLETMVEHAWNWHKEHP 323 W P + SLE +V HAW W ++P Sbjct: 296 WRPAFASLEQIVRHAWQWELQYP 318 Lambda K H 0.317 0.135 0.411 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: 327 Number of extensions: 9 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: 334 Length of database: 321 Length adjustment: 28 Effective length of query: 306 Effective length of database: 293 Effective search space: 89658 Effective search space used: 89658 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate PP_3129 PP_3129 (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.16405.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-128 414.1 0.0 2.5e-128 413.5 0.0 1.2 1 lcl|FitnessBrowser__Putida:PP_3129 PP_3129 UDP-glucose 4-epimerase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3129 PP_3129 UDP-glucose 4-epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.5 0.0 2.5e-128 2.5e-128 2 327 .. 3 316 .. 2 320 .. 0.98 Alignments for each domain: == domain 1 score: 413.5 bits; conditional E-value: 2.5e-128 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeekidaviH 76 Lv+GgaGyiGsh+v++ll++g+ev+v D +s g +++ + d+ad+++l+ ++ ++dav H lcl|FitnessBrowser__Putida:PP_3129 3 YLVVGGAGYIGSHMVKHLLAAGHEVLVADLVSPGPG--IQWAK---------LDIADEAALDVLFGVCRFDAVFH 66 59***************************9999964..55555.........79********************* PP TIGR01179 77 faaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesplnpinpYGrsklm 151 fa++i+vgEsv++P kYY+nnv +tl+Ll+am++ag+++l+FsssaavYg+++ vpi E+++ +pinpYG sk m lcl|FitnessBrowser__Putida:PP_3129 67 FASFIQVGESVSAPGKYYQNNVAATLSLLQAMVNAGIRHLVFSSSAAVYGNPQYVPIDEAHTKGPINPYGLSKWM 141 *************************************************************************** PP TIGR01179 152 vErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkrekleifGtdyptkDGtcvR 226 vE+il+d+ +a ++lk v+LRYFn+aGAd+eg++Ge+++++thli+l++++a+g+re++++fG dy+t+DGtc+R lcl|FitnessBrowser__Putida:PP_3129 142 VEQILEDFDRA-YGLKSVSLRYFNAAGADPEGQLGERHEPETHLIPLILQAASGRREAVTVFGRDYDTPDGTCIR 215 ***********.*************************************************************** PP TIGR01179 227 DyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRaGDpaslvadaski 301 Dy+Hv Dla+aH a+++l +gge +++nlG+g gfsv++vi+++++v+g++i++ a+rRaGDp++lvadask+ lcl|FitnessBrowser__Putida:PP_3129 216 DYVHVADLAAAHALAVDYLLDGGERAAFNLGNGLGFSVQQVIDTARAVTGRQITALDAQRRAGDPPRLVADASKA 290 *************************************************************************** PP TIGR01179 302 krelgwkpkyddLeeiiksawdWekk 327 ++lgw+p + Le+i++ aw+We + lcl|FitnessBrowser__Putida:PP_3129 291 MQVLGWRPAFASLEQIVRHAWQWELQ 316 ***********************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (321 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: 8.92 // [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