Align phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31) (characterized)
to candidate WP_015412496.1 MM_RS12300 phosphoribosyl-ATP pyrophosphatase
Query= reanno::Putida:PP_5015 (111 letters) >NCBI__GCF_000007065.1:WP_015412496.1 Length = 104 Score = 74.7 bits (182), Expect = 3e-19 Identities = 39/93 (41%), Positives = 65/93 (69%), Gaps = 6/93 (6%) Query: 5 LNRLAEVLEERKQAAPDSSYVASL--YHKGLNKILEKLGEESVETIIAAKDAQISKDYSD 62 LNR+ +++ +RK+ ++SYV L + KG+NKILEK+GEES+ETI+A + ++D+ + Sbjct: 9 LNRVYDIILDRKENYDENSYVCKLLNHRKGMNKILEKVGEESIETILAVR----NEDHRE 64 Query: 63 VIYETADLWFHSLVMLSALGQHPQAVLDELERR 95 ++ E++DL FH LV+L+A + + DEL R Sbjct: 65 IVSESSDLIFHLLVLLAANNITLEEIADELSTR 97 Lambda K H 0.312 0.128 0.349 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: 52 Number of extensions: 3 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: 111 Length of database: 104 Length adjustment: 12 Effective length of query: 99 Effective length of database: 92 Effective search space: 9108 Effective search space used: 9108 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.0 bits) S2: 40 (20.0 bits)
Align candidate WP_015412496.1 MM_RS12300 (phosphoribosyl-ATP pyrophosphatase)
to HMM TIGR03188 (hisE: phosphoribosyl-ATP diphosphatase (EC 3.6.1.31))
# 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/TIGR03188.hmm # target sequence database: /tmp/gapView.26159.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03188 [M=84] Accession: TIGR03188 Description: histidine_hisI: phosphoribosyl-ATP diphosphatase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-31 94.5 1.4 2e-31 94.3 1.4 1.0 1 lcl|NCBI__GCF_000007065.1:WP_015412496.1 MM_RS12300 phosphoribosyl-ATP py Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007065.1:WP_015412496.1 MM_RS12300 phosphoribosyl-ATP pyrophosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 94.3 1.4 2e-31 2e-31 1 84 [] 9 94 .. 9 94 .. 0.97 Alignments for each domain: == domain 1 score: 94.3 bits; conditional E-value: 2e-31 TIGR03188 1 leeLeevieerkeedpeeSytakllek..gedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVl 69 l++++++i +rke+ +e+Sy+ kll++ g +kil+KvgEE++E+i+a+ ned+ e+v+E++Dl++hllVl lcl|NCBI__GCF_000007065.1:WP_015412496.1 9 LNRVYDIILDRKENYDENSYVCKLLNHrkGMNKILEKVGEESIETILAVRNEDHREIVSESSDLIFHLLVL 79 789*********************98777****************************************** PP TIGR03188 70 laekgvsledvlaeL 84 la+++++le++++eL lcl|NCBI__GCF_000007065.1:WP_015412496.1 80 LAANNITLEEIADEL 94 ************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (104 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: 00:00:00.00 # Mc/sec: 3.55 // [ok]
This GapMind analysis is from Apr 10 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