Align phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19) (characterized)
to candidate YP_001326736.1 Smed_1048 phosphoribosyl-AMP cyclohydrolase
Query= BRENDA::Q8YH95 (139 letters) >NCBI__GCF_000017145.1:YP_001326736.1 Length = 151 Score = 186 bits (472), Expect = 1e-52 Identities = 89/133 (66%), Positives = 103/133 (77%) Query: 4 FPAQPSDKKAVEEGAAFMPRFDASGLITAIVTDARDGELLMVAHMNEEALRLTLETGIAH 63 F + P +K +E G AF PRFD GLITA+VTDA DG LLMVAHMN EAL LTLETG+AH Sbjct: 6 FASPPQNKSDLETGPAFTPRFDEKGLITAVVTDAGDGALLMVAHMNAEALALTLETGVAH 65 Query: 64 YWSRSRKTLWKKGETSGNLQSVVELRTDCDQDALWLKVHVAGDGPTCHTGRRSCFYRQVV 123 Y+SRSR+ LWKKGE+SGN+Q+V E+RTDCDQDA+WLKV VAG TCHTGRRSCFYR V Sbjct: 66 YYSRSRRRLWKKGESSGNVQAVREIRTDCDQDAIWLKVSVAGHDATCHTGRRSCFYRTVG 125 Query: 124 SSGGKVALTMASD 136 G+ L + D Sbjct: 126 VDEGQAKLVITDD 138 Lambda K H 0.318 0.131 0.396 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: 118 Number of extensions: 2 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: 139 Length of database: 151 Length adjustment: 16 Effective length of query: 123 Effective length of database: 135 Effective search space: 16605 Effective search space used: 16605 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: 42 (20.8 bits)
Align candidate YP_001326736.1 Smed_1048 (phosphoribosyl-AMP cyclohydrolase)
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.19557.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-38 114.7 0.4 9.2e-38 114.3 0.4 1.2 1 lcl|NCBI__GCF_000017145.1:YP_001326736.1 Smed_1048 phosphoribosyl-AMP cyc Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017145.1:YP_001326736.1 Smed_1048 phosphoribosyl-AMP cyclohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 114.3 0.4 9.2e-38 9.2e-38 1 74 [] 46 121 .. 46 121 .. 0.97 Alignments for each domain: == domain 1 score: 114.3 bits; conditional E-value: 9.2e-38 PRA-CH 1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkg..aaCHt 67 m+a+mn+eal+ tletg a+yySrsr++lwkkGe+sgnvq v+eir+dcD+Da++lkv+ +g a+CHt lcl|NCBI__GCF_000017145.1:YP_001326736.1 46 MVAHMNAEALALTLETGVAHYYSRSRRRLWKKGESSGNVQAVREIRTDCDQDAIWLKVSVAGhdATCHT 114 9********************************************************99997557**** PP PRA-CH 68 gersCFy 74 g+rsCFy lcl|NCBI__GCF_000017145.1:YP_001326736.1 115 GRRSCFY 121 ******7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (151 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: 3.84 // [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