Align UTP--glucose-1-phosphate uridylyltransferase; EC 2.7.7.9 (characterized)
to candidate 6938102 Sama_2223 UTP--glucose-1-phosphate uridylyltransferase (RefSeq)
Query= CharProtDB::CH_021667 (302 letters) >FitnessBrowser__SB2B:6938102 Length = 302 Score = 418 bits (1075), Expect = e-122 Identities = 211/293 (72%), Positives = 241/293 (82%), Gaps = 2/293 (0%) Query: 6 TKVKKAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLVTHSSK 65 TK++KAVIPVAGLGTRMLPATKAIPKEMLP+VDKPLIQYVV+E +AAGI EIVLVTH+SK Sbjct: 4 TKIRKAVIPVAGLGTRMLPATKAIPKEMLPVVDKPLIQYVVSEAVAAGIKEIVLVTHASK 63 Query: 66 NSIENHFDTSFELEAMLEKRVKRQLLDEVQSICPPHVTIMQVRQGLAKGLGHAVLCAHPV 125 NSIENHFDTSFELEA LE+RVKRQLLDEVQ+ICP VT++ VRQ AKGLGHA+LCA PV Sbjct: 64 NSIENHFDTSFELEAQLERRVKRQLLDEVQAICPKDVTVISVRQAQAKGLGHAILCARPV 123 Query: 126 VGDEPVAVILPDVILDEYESDLSQDNLAEMIRRFDETGHSQIMVEPVAD--VTAYGVVDC 183 VGDEP AV+LPDVI+D +SDL+ +NLA M+R FDET QIMVE V V YG+ D Sbjct: 124 VGDEPFAVLLPDVIIDGAKSDLTSENLAAMVRLFDETSTGQIMVEAVPHEMVNQYGIADV 183 Query: 184 KGVELAPGESVPMVGVVEKPKADVAPSNLAIVGRYVLSADIWPLLAKTPPGAGDEIQLTD 243 KG ++ G+SVP+ +VEKP D APSNLA+VGRYVL ADIWPLLA+TP GAGDEIQLTD Sbjct: 184 KGHQMVNGDSVPLEALVEKPAVDEAPSNLAVVGRYVLPADIWPLLARTPAGAGDEIQLTD 243 Query: 244 AIDMLIEKETVEAYHMKGKSHDCGNKLGYMQAFVEYGIRHNTLGTEFKAWLEE 296 AI ML+E V AY M GKSHDCGNK GYMQA VEY +RH LG EF +L++ Sbjct: 244 AIAMLMESAQVNAYGMVGKSHDCGNKQGYMQANVEYALRHPELGKEFAKYLKQ 296 Lambda K H 0.317 0.135 0.391 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: 378 Number of extensions: 19 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: 302 Length of database: 302 Length adjustment: 27 Effective length of query: 275 Effective length of database: 275 Effective search space: 75625 Effective search space used: 75625 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 6938102 Sama_2223 (UTP--glucose-1-phosphate uridylyltransferase (RefSeq))
to HMM TIGR01099 (galU: UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9))
# 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/TIGR01099.hmm # target sequence database: /tmp/gapView.13080.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01099 [M=261] Accession: TIGR01099 Description: galU: UTP--glucose-1-phosphate uridylyltransferase 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-115 371.0 0.2 2.1e-115 370.8 0.2 1.0 1 lcl|FitnessBrowser__SB2B:6938102 Sama_2223 UTP--glucose-1-phospha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938102 Sama_2223 UTP--glucose-1-phosphate uridylyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.8 0.2 2.1e-115 2.1e-115 1 261 [] 6 275 .. 6 275 .. 0.97 Alignments for each domain: == domain 1 score: 370.8 bits; conditional E-value: 2.1e-115 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyeleaklek 77 irkaviP+aGlGtr+LPatkaiPkemlp+vdkPliqyvv eav+aGi+eivlvt+ sk++ie+hfDts+elea+le+ lcl|FitnessBrowser__SB2B:6938102 6 IRKAVIPVAGLGTRMLPATKAIPKEMLPVVDKPLIQYVVSEAVAAGIKEIVLVTHASKNSIENHFDTSFELEAQLER 82 89*************************************************************************** PP TIGR01099 78 knkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee.....alkqlielyek 148 + k++ll+ev++i+++ +t++ vrq +akGLGha+l+a+++vgdepfavll+D++++ ++ +l+ +++l+++ lcl|FitnessBrowser__SB2B:6938102 83 RVKRQLLDEVQAICPKdVTVISVRQAQAKGLGHAILCARPVVGDEPFAVLLPDVIIDGAKSdltseNLAAMVRLFDE 159 ***************99***************************************98877788889********** PP TIGR01099 149 tgasiiaveevpkeevskYGvidgee...veeelyevkdlvekPkpeeapsnlaivGrYvltpeifelleetkaGkg 222 t + +i+ve vp+e v++YG++d+++ v+ + + +++lvekP ++eapsnla+vGrYvl ++i+ ll++t+aG+g lcl|FitnessBrowser__SB2B:6938102 160 TSTGQIMVEAVPHEMVNQYGIADVKGhqmVNGDSVPLEALVEKPAVDEAPSNLAVVGRYVLPADIWPLLARTPAGAG 236 *********************998763347788888***************************************** PP TIGR01099 223 geiqltDalrlllekeevlavklkgkryDvGdklgylka 261 +eiqltDa+++l+e+ +v a+ + gk++D+G+k+gy++a lcl|FitnessBrowser__SB2B:6938102 237 DEIQLTDAIAMLMESAQVNAYGMVGKSHDCGNKQGYMQA 275 *************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (302 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: 11.57 // [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