Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_005458261.1 SACCYDRAFT_RS17700 UDP-glucose 4-epimerase GalE
Query= SwissProt::P21977 (332 letters) >NCBI__GCF_000244975.1:WP_005458261.1 Length = 332 Score = 286 bits (731), Expect = 7e-82 Identities = 162/318 (50%), Positives = 206/318 (64%), Gaps = 7/318 (2%) Query: 1 MAILVLGGAGYIGSHMVDRLVEKGQEKVVVVDSLVTGHRAAVHPDAIFYQGDLSDQDFMR 60 M ++V GGAGYIGS RL+E G E V VVD L TGH AV A F QGD ++ Sbjct: 12 MKLVVTGGAGYIGSVCTARLLEAGHE-VTVVDDLSTGHADAVPEGARFVQGDAAE--VAG 68 Query: 61 KVFKENPDVDAVIHFAAYSLVGESMEKPLKYFDNNTAGMVKLLEVMNECGVKYIVFSSTA 120 + E D V+HFAA SLVGESM+ P Y+ N ++LL+ M GV +VFSSTA Sbjct: 69 TLLAEG--FDGVLHFAAKSLVGESMQDPSTYWRGNVLTSLRLLDAMRTHGVSRLVFSSTA 126 Query: 121 ATYGIPEEIPILETTPQNPINPYGESKLMMETIMKWSDQAYGIKYVPLRYFNVAGANLMV 180 ATYG PE PI ET P P N YG +KL ++ + +A+G+ V LRYFNVAGA Sbjct: 127 ATYGEPEVTPIPETAPTAPTNTYGATKLAIDHAITSYARAHGLAAVSLRYFNVAGAYGNY 186 Query: 181 RLVRTRSETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADAHLLAVEY 240 R +ETHL+P+ILQVA G R ++ I+GDDY T DGT +RDY+H DLADAHLLA+ + Sbjct: 187 G-ERHTTETHLIPLILQVATGHRAQVQIYGDDYPTEDGTAIRDYIHVVDLADAHLLALAH 245 Query: 241 LRKGNESTAFNLGSSTGFSNLQILEAARKVTGKEIPAEKADRRPGDPDILIASSEKARTV 300 + G E FNLG+ TGFS Q+++A R VTG EIPA A RR GDP +L+A+S+KA+ Sbjct: 246 AKPG-EHEIFNLGNGTGFSVRQVIDACRSVTGHEIPAAVAQRRVGDPAVLVAASDKAQDE 304 Query: 301 LGWKPQFDNIEKIIASAW 318 LGWKP+ ++ I+A AW Sbjct: 305 LGWKPRHTDLSGIVADAW 322 Lambda K H 0.318 0.136 0.401 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: 294 Number of extensions: 9 Number of successful extensions: 5 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: 332 Length of database: 332 Length adjustment: 28 Effective length of query: 304 Effective length of database: 304 Effective search space: 92416 Effective search space used: 92416 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_005458261.1 SACCYDRAFT_RS17700 (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.20727.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-119 382.1 0.0 1e-118 381.9 0.0 1.0 1 lcl|NCBI__GCF_000244975.1:WP_005458261.1 SACCYDRAFT_RS17700 UDP-glucose 4 Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000244975.1:WP_005458261.1 SACCYDRAFT_RS17700 UDP-glucose 4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.9 0.0 1e-118 1e-118 1 330 [. 13 330 .. 13 332 .] 0.97 Alignments for each domain: == domain 1 score: 381.9 bits; conditional E-value: 1e-118 TIGR01179 1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleee 69 k++vtGgaGyiGs + lle+g+ev v+D+ls+g+++a++++ +v+gd ++++ +l +e lcl|NCBI__GCF_000244975.1:WP_005458261.1 13 KLVVTGGAGYIGSVCTARLLEAGHEVTVVDDLSTGHADAVPEGA-----RFVQGDA---AEVAGTLLAE 73 589****************************************9.....5***975...66889999** PP TIGR01179 70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEesp 138 +d v+Hfaa+ vgEs+++P Y++ nv +l+Ll+am+++gv +l+Fss+aa+Yge+e +pi E++p lcl|NCBI__GCF_000244975.1:WP_005458261.1 74 GFDGVLHFAAKSLVGESMQDPSTYWRGNVLTSLRLLDAMRTHGVSRLVFSSTAATYGEPEVTPIPETAP 142 ********************************************************************* PP TIGR01179 139 lnpinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkr 207 ++p+n YG++kl++++ ++ +++a ++l v+LRYFnvaGA g+ Ge+++++thli+l+++va+g+r lcl|NCBI__GCF_000244975.1:WP_005458261.1 143 TAPTNTYGATKLAIDHAITSYARA-HGLAAVSLRYFNVAGAY--GNYGERHTTETHLIPLILQVATGHR 208 ************************.***************97..788********************** PP TIGR01179 208 ekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsg 276 +++i+G+dypt+DGt++RDyiHv Dla+aHl al + ge e++nlG+g+gfsv++vi+a+++v+g lcl|NCBI__GCF_000244975.1:WP_005458261.1 209 AQVQIYGDDYPTEDGTAIRDYIHVVDLADAHLLALAHAK-PGEHEIFNLGNGTGFSVRQVIDACRSVTG 276 ***********************************9987.5899************************* PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklke 330 ++i++ +a+rR GDpa+lva ++k+++elgwkp+++dL i+++aw+++++++e lcl|NCBI__GCF_000244975.1:WP_005458261.1 277 HEIPAAVAQRRVGDPAVLVAASDKAQDELGWKPRHTDLSGIVADAWEFTQRRQE 330 ************************************************999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (332 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: 12.13 // [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