Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_011385703.1 AMB_RS16910 ATP phosphoribosyltransferase
Query= reanno::azobra:AZOBR_RS19500 (222 letters) >NCBI__GCF_000009985.1:WP_011385703.1 Length = 219 Score = 342 bits (876), Expect = 4e-99 Identities = 170/216 (78%), Positives = 190/216 (87%) Query: 1 VSASQPLVLALPKGRILKELRPLLAHAGIEPEAAFDDADSRLLRFATNIPNLSIIRVRSF 60 +S LV+ALPKGRIL E PL+ AGI PE AFDD SRLLRF TN P++ IIRVRSF Sbjct: 1 MSPQDKLVIALPKGRILDEAMPLVRAAGILPEPAFDDPKSRLLRFGTNHPHIDIIRVRSF 60 Query: 61 DVATFVAFGAAHLGVAGNDVLMEFDYPEIYAPLDLGIGKCRLSVAEPVELGESDDPSRWS 120 DVATFVAFGAAHLGVAGNDVLMEFDYPEIYAPLDLGIG CRLSVAEP +L SDDP RWS Sbjct: 61 DVATFVAFGAAHLGVAGNDVLMEFDYPEIYAPLDLGIGACRLSVAEPDDLAASDDPRRWS 120 Query: 121 HVRVATKYPEVTRKHFAARGVQAECVKLNGAMELAPTLGLCRRIVDLVSTGSTLKANGLV 180 HVR+ATKYPEVT++HFAARGVQAECVKLNGAMELAP+LGLC RIVDLVS+G+TLKANGL Sbjct: 121 HVRIATKYPEVTKRHFAARGVQAECVKLNGAMELAPSLGLCTRIVDLVSSGATLKANGLK 180 Query: 181 EIEHIADVTSRLIVNRAAFKTRPEEISGWIDRFREA 216 E+E +A+VTSRLIVNRAA KTRP+E++GWI+ FR+A Sbjct: 181 EVEVLAEVTSRLIVNRAALKTRPDEMAGWIEAFRKA 216 Lambda K H 0.321 0.137 0.398 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: 245 Number of extensions: 4 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: 222 Length of database: 219 Length adjustment: 22 Effective length of query: 200 Effective length of database: 197 Effective search space: 39400 Effective search space used: 39400 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate WP_011385703.1 AMB_RS16910 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))
# 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.aa/TIGR00070.hmm # target sequence database: /tmp/gapView.31597.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00070 [M=183] Accession: TIGR00070 Description: hisG: ATP phosphoribosyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-56 174.8 0.0 9.9e-56 174.6 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011385703.1 AMB_RS16910 ATP phosphoribosyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385703.1 AMB_RS16910 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 174.6 0.0 9.9e-56 9.9e-56 1 183 [] 7 194 .. 7 194 .. 0.93 Alignments for each domain: == domain 1 score: 174.6 bits; conditional E-value: 9.9e-56 TIGR00070 1 lriAlpKGrleeetlkllekaglk....lskkeerkliasaedeevevlllrakdiptyvekgaadlGi 65 l iAlpKGr+++e++ l ++ag+ + ++++r l + +++++++++ +r+ d++t+v+ gaa+lG+ lcl|NCBI__GCF_000009985.1:WP_011385703.1 7 LVIALPKGRILDEAMPLVRAAGILpepaFDDPKSRLLRFGTNHPHIDIIRVRSFDVATFVAFGAAHLGV 75 679******************99744446677799********************************** PP TIGR00070 66 tGkDlleE.seadvvelldlgfgkcklvlAvpees.dvesledlkegkriATkypnltreylekkgvkv 132 G D+l+E ++++++ ldlg+g+c+l++A p++ + +++ + + riATkyp++t+++++ +gv++ lcl|NCBI__GCF_000009985.1:WP_011385703.1 76 AGNDVLMEfDYPEIYAPLDLGIGACRLSVAEPDDLaASDDPRRWS-HVRIATKYPEVTKRHFAARGVQA 143 ********99999*********************95555655666.78********************* PP TIGR00070 133 eivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 e+vkl+Ga+Elap+lgl IvD+v++G+tL++ngLk++e++ e+++rli+ lcl|NCBI__GCF_000009985.1:WP_011385703.1 144 ECVKLNGAMELAPSLGLCTRIVDLVSSGATLKANGLKEVEVLAEVTSRLIV 194 *************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (219 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.68 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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