Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate N515DRAFT_2700 N515DRAFT_2700 UTP--glucose-1-phosphate uridylyltransferase
Query= BRENDA::Q8PK83 (297 letters) >FitnessBrowser__Dyella79:N515DRAFT_2700 Length = 291 Score = 371 bits (952), Expect = e-107 Identities = 194/288 (67%), Positives = 222/288 (77%), Gaps = 2/288 (0%) Query: 1 MSQRIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNR 60 MS+ +RK VFPVAGLGTRFLPATK V KEMLP++DKPLIQYAVDEA+ AG DTL+FVTNR Sbjct: 1 MSKPLRKVVFPVAGLGTRFLPATKVVAKEMLPVLDKPLIQYAVDEAVDAGADTLVFVTNR 60 Query: 61 YKHSIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAK 120 YKH+IADYFDKAYELE KL+ GK E L LV+ LP VRAIFVTQ EALGLGHAVLCAK Sbjct: 61 YKHAIADYFDKAYELEAKLQEKGKDELLALVQGTLPRNVRAIFVTQPEALGLGHAVLCAK 120 Query: 121 AVVGNEPFAVLLPDDLMWNRGDAALTQMANVAEASG-GSVIAVEDVPHDKTASYGIVSTD 179 VVG+EPF V+LPDDL+WN+G AL QMA +A+ G G VIAVE+VP T YGIV Sbjct: 121 PVVGDEPFGVILPDDLIWNQGKGALGQMAELAQGQGAGGVIAVEEVPQTDTDKYGIVDAT 180 Query: 180 AFDGRKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAE 239 D R +I +VEKPKP APSNLAVVGRYVL +IF+LLE T GAGGEIQLTDAI Sbjct: 181 PIDPRSAQIRHMVEKPKPSEAPSNLAVVGRYVLPGRIFELLEKTTPGAGGEIQLTDAIDA 240 Query: 240 LLKEE-QVDAFRFEGRRFDCGAHIGLIEATVHFALEHEKHGGPAKEIL 286 LLKE+ +V A+RFEG RFDCG GL+ AT+H AL+ K +E+L Sbjct: 241 LLKEQGKVLAYRFEGTRFDCGNKAGLVRATMHMALQDPKLAPVVRELL 288 Lambda K H 0.319 0.137 0.393 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: 332 Number of extensions: 9 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: 297 Length of database: 291 Length adjustment: 26 Effective length of query: 271 Effective length of database: 265 Effective search space: 71815 Effective search space used: 71815 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate N515DRAFT_2700 N515DRAFT_2700 (UTP--glucose-1-phosphate uridylyltransferase)
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.23346.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-104 334.5 0.0 2.8e-104 334.3 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2700 N515DRAFT_2700 UTP--glucose-1-ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2700 N515DRAFT_2700 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 334.3 0.0 2.8e-104 2.8e-104 1 261 [] 5 269 .. 5 269 .. 0.96 Alignments for each domain: == domain 1 score: 334.3 bits; conditional E-value: 2.8e-104 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfD 66 +rk+v+P+aGlGtr+LPatk + kemlp++dkPliqy+v+eav+aG + +v+vt+r k+ai d+fD lcl|FitnessBrowser__Dyella79:N515DRAFT_2700 5 LRKVVFPVAGLGTRFLPATKVVAKEMLPVLDKPLIQYAVDEAVDAGADTLVFVTNRYKHAIADYFD 70 59**************************************************************** PP TIGR01099 67 tsyeleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdl 131 ++yeleakl++k+k+ell v+ ++ ++ ++v q ea GLGhavl+a+++vgdepf v+l+Ddl lcl|FitnessBrowser__Dyella79:N515DRAFT_2700 71 KAYELEAKLQEKGKDELLALVQGTLPRnVRAIFVTQPEALGLGHAVLCAKPVVGDEPFGVILPDDL 136 **********************988877*************************************9 PP TIGR01099 132 vseeee.alkqlielyektga.siiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeap 195 + ++ + al q+ el + ga +iaveevp+++++kYG++d++ ++ + +++++vekPkp eap lcl|FitnessBrowser__Dyella79:N515DRAFT_2700 137 IWNQGKgALGQMAELAQGQGAgGVIAVEEVPQTDTDKYGIVDATPIDPRSAQIRHMVEKPKPSEAP 202 9988766*******99987763699***************************************** PP TIGR01099 196 snlaivGrYvltpeifelleetkaGkggeiqltDalrlllek.eevlavklkgkryDvGdklgylk 260 snla+vGrYvl +ifelle+t +G+ggeiqltDa++ ll++ +vla++++g+r+D+G+k g ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2700 203 SNLAVVGRYVLPGRIFELLEKTTPGAGGEIQLTDAIDALLKEqGKVLAYRFEGTRFDCGNKAGLVR 268 *************************************98865169******************987 PP TIGR01099 261 a 261 a lcl|FitnessBrowser__Dyella79:N515DRAFT_2700 269 A 269 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (291 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: 8.34 // [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