Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate WP_022950095.1 H035_RS0116655 UTP--glucose-1-phosphate uridylyltransferase
Query= BRENDA::Q8PK83 (297 letters) >NCBI__GCF_000421465.1:WP_022950095.1 Length = 289 Score = 347 bits (889), Expect = e-100 Identities = 169/272 (62%), Positives = 213/272 (78%) Query: 4 RIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNRYKH 63 +I+KAVFPVAGLGTRFLPATK PKEMLP++DKPLIQYAV+EA AG + ++FVT R K Sbjct: 2 KIKKAVFPVAGLGTRFLPATKASPKEMLPVVDKPLIQYAVEEAAAAGIELMVFVTGRNKT 61 Query: 64 SIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAKAVV 123 +I+++FDKAYELE +LE GK+++LELVR+ P GV +++ QAEALGLGHAVLCAK ++ Sbjct: 62 AISNHFDKAYELETELEHRGKIDKLELVRNIPPAGVNCVYIRQAEALGLGHAVLCAKPII 121 Query: 124 GNEPFAVLLPDDLMWNRGDAALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDAFDG 183 GNEPFAVLL DDL+ N G + +M + E+ G SV+AVE++P D + SYG+V+ Sbjct: 122 GNEPFAVLLADDLIENNGRGCMEEMVEIYESHGRSVLAVEEIPLDASESYGVVAASEVVD 181 Query: 184 RKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAELLKE 243 R+ IVEKPKPE APSNL VVGRY+L+P+IFDLLE G GAGGEIQLTDAIA+LL+ Sbjct: 182 NVTRVEGIVEKPKPEEAPSNLGVVGRYILTPRIFDLLETVGRGAGGEIQLTDAIAQLLEH 241 Query: 244 EQVDAFRFEGRRFDCGAHIGLIEATVHFALEH 275 E V A RF G+R+DCGA +G +EATV AL+H Sbjct: 242 ELVYAHRFSGKRYDCGAKLGYLEATVDHALQH 273 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: 290 Number of extensions: 12 Number of successful extensions: 1 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: 289 Length adjustment: 26 Effective length of query: 271 Effective length of database: 263 Effective search space: 71273 Effective search space used: 71273 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 WP_022950095.1 H035_RS0116655 (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.30502.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-117 375.1 0.0 1.1e-116 374.9 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022950095.1 H035_RS0116655 UTP--glucose-1-ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022950095.1 H035_RS0116655 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 374.9 0.0 1.1e-116 1.1e-116 1 261 [] 3 265 .. 3 265 .. 0.99 Alignments for each domain: == domain 1 score: 374.9 bits; conditional E-value: 1.1e-116 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsy 69 i+kav+P+aGlGtr+LPatka Pkemlp+vdkPliqy+veea +aGie +v+vtgr+k+ai +hfD++y lcl|NCBI__GCF_000421465.1:WP_022950095.1 3 IKKAVFPVAGLGTRFLPATKASPKEMLPVVDKPLIQYAVEEAAAAGIELMVFVTGRNKTAISNHFDKAY 71 89******************************************************************* PP TIGR01099 70 eleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee 137 ele++le+++k + l+ vr+i + ++++y+rq ea GLGhavl+a++++g+epfavll+Ddl++++ + lcl|NCBI__GCF_000421465.1:WP_022950095.1 72 ELETELEHRGKIDKLELVRNIPPAgVNCVYIRQAEALGLGHAVLCAKPIIGNEPFAVLLADDLIENNGR 140 **********************999***************************************99977 PP TIGR01099 138 .alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYv 205 ++++++e+ye g s++avee+p + ++YGv++++ev +++++v+ +vekPkpeeapsnl +vGrY+ lcl|NCBI__GCF_000421465.1:WP_022950095.1 141 gCMEEMVEIYESHGRSVLAVEEIPLDASESYGVVAASEVVDNVTRVEGIVEKPKPEEAPSNLGVVGRYI 209 7******************************************************************** PP TIGR01099 206 ltpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 ltp+if+lle++ +G+ggeiqltDa+++lle+e v+a++++gkryD+G klgyl+a lcl|NCBI__GCF_000421465.1:WP_022950095.1 210 LTPRIFDLLETVGRGAGGEIQLTDAIAQLLEHELVYAHRFSGKRYDCGAKLGYLEA 265 ******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (289 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: 00:00:00.01 # Mc/sec: 7.19 // [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