Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate RR42_RS15100 RR42_RS15100 UTP--glucose-1-phosphate uridylyltransferase
Query= BRENDA::Q8PK83 (297 letters) >FitnessBrowser__Cup4G11:RR42_RS15100 Length = 292 Score = 293 bits (751), Expect = 2e-84 Identities = 152/275 (55%), Positives = 196/275 (71%), Gaps = 1/275 (0%) Query: 1 MSQRIRKAVFPVAGLGTRFLPATKTVPKEMLPIIDKPLIQYAVDEAIQAGCDTLIFVTNR 60 M R+ KAVFPVAGLGTRFLPATK PKEMLP++DKPLIQYAV+EA+ AG +IFVT R Sbjct: 1 METRVTKAVFPVAGLGTRFLPATKASPKEMLPVVDKPLIQYAVEEAMAAGITEMIFVTGR 60 Query: 61 YKHSIADYFDKAYELEQKLERAGKLEQLELVRHALPDGVRAIFVTQAEALGLGHAVLCAK 120 K +I D+FDKAYELE +LE K L LVR P V +V Q EALGLGHAVLCA+ Sbjct: 61 SKRAIEDHFDKAYELEAELEAKNKQALLSLVRSIKPSHVECFYVRQPEALGLGHAVLCAE 120 Query: 121 AVVGNEPFAVLLPDDLMWNRGDAALTQMANVAEASGGSVIAVEDVPHDKTASYGIVSTDA 180 +VG+ PFAV+L DDL+ + + QM ++ SV+ VE++ +++ SYG+V Sbjct: 121 KLVGDAPFAVMLADDLL-DGNPPVMKQMVDLYGHYNCSVLGVEEIAPEQSRSYGVVDGRE 179 Query: 181 FDGRKGRINAIVEKPKPEVAPSNLAVVGRYVLSPKIFDLLEATGAGAGGEIQLTDAIAEL 240 +D +++ IVEKP PE APSNL VVGRY+L+P+IFD + GAGGE QLTDAI L Sbjct: 180 WDEGVIKVSNIVEKPAPENAPSNLGVVGRYILTPRIFDHIRNLKPGAGGEFQLTDAIQSL 239 Query: 241 LKEEQVDAFRFEGRRFDCGAHIGLIEATVHFALEH 275 L +EQV A+R++G R+DCG+ +G ++ATV FAL+H Sbjct: 240 LSQEQVLAYRYKGVRYDCGSKLGYLKATVEFALKH 274 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: 260 Number of extensions: 5 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: 297 Length of database: 292 Length adjustment: 26 Effective length of query: 271 Effective length of database: 266 Effective search space: 72086 Effective search space used: 72086 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 RR42_RS15100 RR42_RS15100 (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.20311.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-120 386.2 0.0 4.8e-120 386.0 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS15100 RR42_RS15100 UTP--glucose-1-phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS15100 RR42_RS15100 UTP--glucose-1-phosphate uridylyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 386.0 0.0 4.8e-120 4.8e-120 1 261 [] 5 266 .. 5 266 .. 0.99 Alignments for each domain: == domain 1 score: 386.0 bits; conditional E-value: 4.8e-120 TIGR01099 1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsy 69 + kav+P+aGlGtr+LPatka Pkemlp+vdkPliqy+veea++aGi+e+++vtgrskraiedhfD++y lcl|FitnessBrowser__Cup4G11:RR42_RS15100 5 VTKAVFPVAGLGTRFLPATKASPKEMLPVVDKPLIQYAVEEAMAAGITEMIFVTGRSKRAIEDHFDKAY 73 679****************************************************************** PP TIGR01099 70 eleaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee 137 elea+le knk+ ll+ vr+i ++ ++++yvrq ea GLGhavl+ae+lvgd pfav+l+Ddl++ + + lcl|FitnessBrowser__Cup4G11:RR42_RS15100 74 ELEAELEAKNKQALLSLVRSIKPShVECFYVRQPEALGLGHAVLCAEKLVGDAPFAVMLADDLLDGNPP 142 **********************988******************************************** PP TIGR01099 138 alkqlielyektgasiiaveevpkeevskYGvidgeeveeelyevkdlvekPkpeeapsnlaivGrYvl 206 ++kq+++ly ++++s+++vee++ e+ ++YGv+dg+e +e +++v+++vekP pe+apsnl +vGrY+l lcl|FitnessBrowser__Cup4G11:RR42_RS15100 143 VMKQMVDLYGHYNCSVLGVEEIAPEQSRSYGVVDGREWDEGVIKVSNIVEKPAPENAPSNLGVVGRYIL 211 ********************************************************************* PP TIGR01099 207 tpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261 tp+if++++++k+G+gge qltDa++ ll++e+vla++ kg ryD+G+klgylka lcl|FitnessBrowser__Cup4G11:RR42_RS15100 212 TPRIFDHIRNLKPGAGGEFQLTDAIQSLLSQEQVLAYRYKGVRYDCGSKLGYLKA 266 *****************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (292 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 10.58 // [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