Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate WP_015738359.1 ADEG_RS01600 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= SwissProt::O26347 (138 letters) >NCBI__GCF_000024605.1:WP_015738359.1 Length = 242 Score = 125 bits (315), Expect = 3e-34 Identities = 60/123 (48%), Positives = 83/123 (67%), Gaps = 1/123 (0%) Query: 15 RHNINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSG 74 R + + LI A+ QD T EVLM+AYMN+EAL +TL +G ++S SR +LW KGE+SG Sbjct: 7 RFKFDAQGLIPAIIQDSRTNEVLMLAYMNKEALAKTLTSGQTWFYSRSRQRLWHKGETSG 66 Query: 75 HVQRVKDVLVDCDGDAVVLKVEQEGGACHTGYRSCFYRSIDGDELKVREDAVKVFDPEEI 134 ++Q V +V DCD DA+++KV Q G ACH GY+SCF+ I+ D +V FDP ++ Sbjct: 67 NIQEVDEVYFDCDADALLIKVRQHGAACHEGYKSCFHYRIEPDG-RVALVGQPAFDPADV 125 Query: 135 YGD 137 YGD Sbjct: 126 YGD 128 Lambda K H 0.318 0.137 0.410 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: 109 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: 138 Length of database: 242 Length adjustment: 19 Effective length of query: 119 Effective length of database: 223 Effective search space: 26537 Effective search space used: 26537 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 44 (21.6 bits)
Align candidate WP_015738359.1 ADEG_RS01600 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE)
to HMM PF01502 (PRA-CH)
# 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/PF01502.22.hmm # target sequence database: /tmp/gapView.25035.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PRA-CH [M=74] Accession: PF01502.22 Description: Phosphoribosyl-AMP cyclohydrolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-41 125.0 0.8 7.3e-41 124.3 0.8 1.4 1 lcl|NCBI__GCF_000024605.1:WP_015738359.1 ADEG_RS01600 bifunctional phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_015738359.1 ADEG_RS01600 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl- # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 124.3 0.8 7.3e-41 7.3e-41 1 74 [] 30 103 .. 30 103 .. 0.99 Alignments for each domain: == domain 1 score: 124.3 bits; conditional E-value: 7.3e-41 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtge 69 mlaymn+eal+ktl++g++++ySrsrq+lw+kGetsgn+q+v e+++dcD+Dall+kv+q+gaaCH+g+ lcl|NCBI__GCF_000024605.1:WP_015738359.1 30 MLAYMNKEALAKTLTSGQTWFYSRSRQRLWHKGETSGNIQEVDEVYFDCDADALLIKVRQHGAACHEGY 98 9******************************************************************** PP PRA-CH 70 rsCFy 74 +sCF+ lcl|NCBI__GCF_000024605.1:WP_015738359.1 99 KSCFH 103 ****6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (242 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: 6.79 // [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