Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_039104092.1 FPB0191_RS03585 UDP-glucose 4-epimerase GalE
Query= BRENDA::P09147 (338 letters) >NCBI__GCF_000807275.1:WP_039104092.1 Length = 338 Score = 439 bits (1129), Expect = e-128 Identities = 210/338 (62%), Positives = 263/338 (77%), Gaps = 1/338 (0%) Query: 1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIR 60 M +LVTGG GYIGSHTCV+LL++G+ II+DNL NSK+SVL IE++ GK P F GD+ Sbjct: 1 MNILVTGGLGYIGSHTCVKLLESGYTPIIVDNLYNSKKSVLYRIEQITGKKPLFYYGDVC 60 Query: 61 NEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFI 120 + + + ++ I VIHFAGLKAVGESV KPL YY+NNV+G++ L M+ V N I Sbjct: 61 DRTFLNTVFEENNIAGVIHFAGLKAVGESVTKPLTYYENNVHGSIVLAQVMQEHQVYNLI 120 Query: 121 FSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNP 180 FSSSATVYGD+ +PYVESF TG+ +PYG SK MVE+I DL K WSI+LLRYFNP Sbjct: 121 FSSSATVYGDKNPVPYVESFETGSITNPYGWSKYMVERIYQDLAKTSSKWSISLLRYFNP 180 Query: 181 VGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLA 240 VGAH SG +GEDPQGIPNNLMPYIAQVA+G+R+ L+I+GNDYPT+DGTGVRDYIHV DLA Sbjct: 181 VGAHASGLIGEDPQGIPNNLMPYIAQVAIGKREKLSIYGNDYPTKDGTGVRDYIHVEDLA 240 Query: 241 DGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYW 300 GHV A+ K N+ GVHIYNLGAG+G+SV DV+ A+ ACGK + Y RR GD+ A+W Sbjct: 241 IGHVAAL-KTMNESGVHIYNLGAGIGSSVFDVLGAYENACGKKLAYQIVGRRAGDIAAFW 299 Query: 301 ADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338 ADASKA++ELNWR L++MA+D+W+WQ+++P GYP+ Sbjct: 300 ADASKAEKELNWRTKYNLNDMAKDSWNWQTKNPNGYPE 337 Lambda K H 0.318 0.136 0.419 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: 437 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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_039104092.1 FPB0191_RS03585 (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.2798844.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-137 442.4 0.2 4.6e-137 442.2 0.2 1.0 1 NCBI__GCF_000807275.1:WP_039104092.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000807275.1:WP_039104092.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.2 0.2 4.6e-137 4.6e-137 1 331 [. 2 334 .. 2 335 .. 0.99 Alignments for each domain: == domain 1 score: 442.2 bits; conditional E-value: 4.6e-137 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeeki 71 +iLvtGg GyiGsh++++lle+g+ +++Dnl +++k++l ++e+it + ++ gd+ d++ l++v+ee++i NCBI__GCF_000807275.1:WP_039104092.1 2 NILVTGGLGYIGSHTCVKLLESGYTPIIVDNLYNSKKSVLYRIEQITgkKPLFYYGDVCDRTFLNTVFEENNI 74 59********************************************998999********************* PP TIGR01179 72 daviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pin 143 viHfa+l+avgEsv++Pl YYennv+++++L ++mq+++v +liFsssa+vYg+++ vp+ E+++++ +n NCBI__GCF_000807275.1:WP_039104092.1 75 AGVIHFAGLKAVGESVTKPLTYYENNVHGSIVLAQVMQEHQVYNLIFSSSATVYGDKNPVPYVESFETGsITN 147 ********************************************************************9789* PP TIGR01179 144 pYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGt 215 pYG sk mvEri +dl+k+ +++++ +LRYFn++GA+ +g iGe++++++ +l++++a+va+gkrekl+i+G+ NCBI__GCF_000807275.1:WP_039104092.1 148 PYGWSKYMVERIYQDLAKTSSKWSISLLRYFNPVGAHASGLIGEDPQGIPnNLMPYIAQVAIGKREKLSIYGN 220 **************************************************9********************** PP TIGR01179 216 dyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRa 288 dyptkDGt+vRDyiHveDla +H+aal++++e +++++ynlGag g sv +v+ a ++++gk++++++ rRa NCBI__GCF_000807275.1:WP_039104092.1 221 DYPTKDGTGVRDYIHVEDLAIGHVAALKTMNE-SGVHIYNLGAGIGSSVFDVLGAYENACGKKLAYQIVGRRA 292 ****************************9986.89************************************** PP TIGR01179 289 GDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331 GD+a+++adask+++el+w++ky+ L+++ k++w+W++k+++g NCBI__GCF_000807275.1:WP_039104092.1 293 GDIAAFWADASKAEKELNWRTKYN-LNDMAKDSWNWQTKNPNG 334 ************************.**************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (338 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: 00:00:00.00 # Mc/sec: 27.05 // [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