Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Ga0059261_1305 Ga0059261_1305 UDP-glucose-4-epimerase GalE
Query= SwissProt::Q7WTB1 (330 letters) >FitnessBrowser__Korea:Ga0059261_1305 Length = 331 Score = 269 bits (688), Expect = 6e-77 Identities = 141/320 (44%), Positives = 196/320 (61%), Gaps = 1/320 (0%) Query: 3 VLVIGGAGYIGSHAVRELVKEGNDVLVLDALYTGHRKAVDPKAKFYQGDIEDTFLVSKIL 62 V+V GGAGYIGSHAV L+ G V+VLD L TG AVDP+A ++ D V + Sbjct: 6 VMVTGGAGYIGSHAVLALLDAGWRVVVLDNLVTGFDWAVDPRANLVVANVADDDKVRAAI 65 Query: 63 RDEKIDAVMHFAAYSLVPESVKKPLKYYDNNVTGMISLLQAMNDANVKYLVFSSSAATYG 122 R+ I A+MHFA +VPESV PLKYY NN SL+++ VK+ +FSS+AATYG Sbjct: 66 REHGITAIMHFAGSVVVPESVSDPLKYYRNNTAASRSLIESAVAEGVKHFIFSSTAATYG 125 Query: 123 IPKKLPITEDTPLNPINPYGETKMMMEKIMAWADKADGIKYTALRYFNVAGASSDGSIGE 182 IPK +P+ ED+P PINPYG +K+M E ++ A + + ALRYFNVAGA G G+ Sbjct: 126 IPKVVPVREDSPQLPINPYGMSKLMTEHMLRDVAAAHPLNFAALRYFNVAGADPQGRSGQ 185 Query: 183 DHAPETHLIPNILKSAISGDGKFTIFGDDYDTKDGTNVRDYVQVEDLIDAHILALKHMM- 241 A THLI +++A ++FG D+ T+DGT VRDY+ V DL AH+ AL ++ Sbjct: 186 STAGATHLIKVAVEAATGKRDGVSVFGTDFATRDGTGVRDYIHVTDLAAAHVDALDLLVA 245 Query: 242 KTNKSDVFNLGTAHGYSNLEILESAKKVTGIDIPYTMGPRRGGDPDSLVADSTKARTVLG 301 + +S N G GYS LE+L++ +VT + I + RR GDPD L++D+ L Sbjct: 246 EPRQSHFLNAGYGRGYSVLEVLDAVDRVTNVKIERRLEGRRAGDPDELISDNRAILEALP 305 Query: 302 WKPKHENVDDVIATAWKWHK 321 W+PKH+++D ++ A W + Sbjct: 306 WRPKHDDLDRIVKDALAWER 325 Lambda K H 0.315 0.134 0.395 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: 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: 330 Length of database: 331 Length adjustment: 28 Effective length of query: 302 Effective length of database: 303 Effective search space: 91506 Effective search space used: 91506 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate Ga0059261_1305 Ga0059261_1305 (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.22350.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-127 411.2 0.0 1.4e-127 411.1 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_1305 Ga0059261_1305 UDP-glucose-4-epi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_1305 Ga0059261_1305 UDP-glucose-4-epimerase GalE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.1 0.0 1.4e-127 1.4e-127 2 329 .. 6 328 .. 5 331 .] 0.98 Alignments for each domain: == domain 1 score: 411.1 bits; conditional E-value: 1.4e-127 TIGR01179 2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekitevklvegdladkekleavleeek 70 ++vtGgaGyiGsh v +ll++g +vvvlDnl++g+ +a+ +lv +++ad k++a+++e+ lcl|FitnessBrowser__Korea:Ga0059261_1305 6 VMVTGGAGYIGSHAVLALLDAGWRVVVLDNLVTGFDWAVDPRA-----NLVVANVADDDKVRAAIREHG 69 89*************************************9888.....6******************** PP TIGR01179 71 idaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139 i a++Hfa+++ v+Esv++PlkYY+nn+ ++ +L+e+ ++ gvk++iFss+aa+Yg ++ vp+ E+sp+ lcl|FitnessBrowser__Korea:Ga0059261_1305 70 ITAIMHFAGSVVVPESVSDPLKYYRNNTAASRSLIESAVAEGVKHFIFSSTAATYGIPKVVPVREDSPQ 138 ********************************************************************* PP TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknathliklvaevavgkre 208 pinpYG sklm+E++l+d++ a + l++++LRYFnvaGAd++g+ G+++ +athlik+++e+a+gkr+ lcl|FitnessBrowser__Korea:Ga0059261_1305 139 LPINPYGMSKLMTEHMLRDVAAA-HPLNFAALRYFNVAGADPQGRSGQSTAGATHLIKVAVEAATGKRD 206 ********************999.9******************************************** PP TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeg.gesevynlGagqgfsvkevieavkkvsg 276 +++fGtd+ t+DGt+vRDyiHv+Dla+aH++al+ l ++ +s+ +n G+g+g+sv+ev++av++v++ lcl|FitnessBrowser__Korea:Ga0059261_1305 207 GVSVFGTDFATRDGTGVRDYIHVTDLAAAHVDALDLLVAEpRQSHFLNAGYGRGYSVLEVLDAVDRVTN 275 ***********************************99877589************************** PP TIGR01179 277 kdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329 ++i+ +l+ rRaGDp +l++d+ i + l w+pk+ddL+ i+k+a++We+kl lcl|FitnessBrowser__Korea:Ga0059261_1305 276 VKIERRLEGRRAGDPDELISDNRAILEALPWRPKHDDLDRIVKDALAWERKLA 328 *************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (332 nodes) Target sequences: 1 (331 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: 00:00:00.01 # Mc/sec: 7.31 // [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