Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_044408447.1 NA59_RS04260 UDP-glucose 4-epimerase GalE
Query= curated2:Q9KDV3 (334 letters) >NCBI__GCF_000934765.1:WP_044408447.1 Length = 337 Score = 344 bits (883), Expect = 2e-99 Identities = 173/328 (52%), Positives = 215/328 (65%), Gaps = 5/328 (1%) Query: 1 MAILVTGGAGYIGSHTVLFLLEQGEQVIVLDNLQKGHAGALSDVTFYHGDIRDDQLLDTI 60 M ILV GGAGYIGSH V L++ G V VLDNL GH GD+ D LLD + Sbjct: 1 MEILVAGGAGYIGSHMVKMLVKAGHVVTVLDNLSTGHRSLAKYGELVEGDLADTALLDNL 60 Query: 61 FTTHSIDTVIHFAANSLVGESVKQPIEYYENNVIGTHTLLKKMLEHDVKKIVFSSTAATY 120 F H V+HFAA SLVGESV P +YY NNV T LL M++HDV IVFSSTAATY Sbjct: 61 FAQHDFKCVVHFAAFSLVGESVTNPAKYYRNNVCNTLNLLDAMVKHDVLNIVFSSTAATY 120 Query: 121 GEPVQIPIQESDPTIPTNPYGETKLAIEKMFHWCQEAYGLQYVCLRYFNAAGADPNGRIG 180 G PV P+ E P P NPYG +KL +E + +AYGL V LRYFNA GADP +G Sbjct: 121 GNPVYTPMDEQHPQSPINPYGASKLMVETLLQVYAKAYGLNSVALRYFNACGADPELELG 180 Query: 181 EDHSPESHLIPIVLQVALGQRERVAIFGDDYQTEDGSCIRDYIHVMDLANAHYLACEHLR 240 E H PE+HLIP+VLQ A G+R+ + IFG+DY TEDG+C+RDYIHV+DL AH LA + + Sbjct: 181 ELHDPETHLIPLVLQAASGRRDSICIFGEDYPTEDGTCVRDYIHVLDLCFAHQLAMQAML 240 Query: 241 KDGQSGS--FNLGNGKGFSVKEVIEVCRQVT---GHPIPAEIAPRRSGDPASLIASSEKA 295 SG+ FNLGNG+GFSVK+VI+ + + G I + A RR GDPA L+A+++KA Sbjct: 241 SGQLSGAHCFNLGNGEGFSVKQVIDAAQAMVAQEGFNIKVQQAERREGDPAVLVANADKA 300 Query: 296 QTILGWEPKYPSLETMVEHAWNWHKEHP 323 + L W+P+Y L T++ HAW W K+ P Sbjct: 301 KQTLNWQPQYTDLTTILRHAWEWEKKQP 328 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: 376 Number of extensions: 17 Number of successful extensions: 3 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: 337 Length adjustment: 28 Effective length of query: 306 Effective length of database: 309 Effective search space: 94554 Effective search space used: 94554 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: 49 (23.5 bits)
Align candidate WP_044408447.1 NA59_RS04260 (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.10756.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-135 437.0 0.0 2.1e-135 436.8 0.0 1.0 1 lcl|NCBI__GCF_000934765.1:WP_044408447.1 NA59_RS04260 UDP-glucose 4-epime Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000934765.1:WP_044408447.1 NA59_RS04260 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.8 0.0 2.1e-135 2.1e-135 2 329 .. 3 328 .. 2 331 .. 0.97 Alignments for each domain: == domain 1 score: 436.8 bits; conditional E-value: 2.1e-135 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 iLv+GgaGyiGsh+v+ l ++g+ v vlDnls+g+++ k++e lvegdlad++ l++++++++ lcl|NCBI__GCF_000934765.1:WP_044408447.1 3 ILVAGGAGYIGSHMVKMLVKAGHVVTVLDNLSTGHRSLAKYGE------LVEGDLADTALLDNLFAQHD 65 9******************************************......******************** PP TIGR01179 71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139 ++ v+Hfaa+ vgEsv++P+kYY+nnv ntl+Ll+am+k+ v +++Fss+aa+Yg++ +p+ E++p+ lcl|NCBI__GCF_000934765.1:WP_044408447.1 66 FKCVVHFAAFSLVGESVTNPAKYYRNNVCNTLNLLDAMVKHDVLNIVFSSTAATYGNPVYTPMDEQHPQ 134 ********************************************************************* PP TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208 +pinpYG+sklmvE +l+ ++ka ++l+ v+LRYFn++GAd+e e+Ge + ++thli+lv+++a+g+r+ lcl|NCBI__GCF_000934765.1:WP_044408447.1 135 SPINPYGASKLMVETLLQVYAKA-YGLNSVALRYFNACGADPELELGELHDPETHLIPLVLQAASGRRD 202 ***********************.********************************************* PP TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeg..gesevynlGagqgfsvkevieavkkvs 275 ++ ifG+dypt+DGtcvRDyiHv Dl aH a++a+ +g ++++ +nlG+g+gfsvk+vi+a+++++ lcl|NCBI__GCF_000934765.1:WP_044408447.1 203 SICIFGEDYPTEDGTCVRDYIHVLDLCFAHQLAMQAMLSGqlSGAHCFNLGNGEGFSVKQVIDAAQAMV 271 ************************************999856799*******************99886 PP TIGR01179 276 ...gkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329 g +ikv+ a+rR+GDpa+lva+a+k+k++l+w+p+y+dL +i++ aw+Wekk++ lcl|NCBI__GCF_000934765.1:WP_044408447.1 272 aqeGFNIKVQQAERREGDPAVLVANADKAKQTLNWQPQYTDLTTILRHAWEWEKKQP 328 3336689**********************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (337 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: 11.63 // [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