Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate 5209751 Shew_2204 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein (RefSeq)
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >FitnessBrowser__PV4:5209751 Length = 206 Score = 233 bits (594), Expect = 2e-66 Identities = 119/194 (61%), Positives = 146/194 (75%), Gaps = 3/194 (1%) Query: 10 LDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSG 69 LDW+K GL+P +VQ+ ++G+VLMLGYMN EAL +TL S K+TFFSR+KQRLWTKGETSG Sbjct: 10 LDWDKQQGLLPAVVQNHLTGKVLMLGYMNQEALAQTLASRKITFFSRSKQRLWTKGETSG 69 Query: 70 NFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGD-TAHQWLFLYQLEQLLAERKSA 128 N L++++I DCDND+LLV P GPTCH SC+ D AH F+ L L+A R+ Sbjct: 70 NTLDLIAIDSDCDNDSLLVQVIPNGPTCHLERESCWPDGEAHP--FIDNLANLIASRRGQ 127 Query: 129 DPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQG 188 D ++SYTA L+ GTKRIAQKVGEEG+ETALAA HD+ EL NEASDL+YHLLVLL+DQ Sbjct: 128 DAKSSYTAHLFERGTKRIAQKVGEEGLETALAAATHDKEELINEASDLIYHLLVLLEDQD 187 Query: 189 LDLTTVIENLRKRH 202 L L + NL RH Sbjct: 188 LSLEDITANLLARH 201 Lambda K H 0.317 0.132 0.384 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: 141 Number of extensions: 3 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: 203 Length of database: 206 Length adjustment: 21 Effective length of query: 182 Effective length of database: 185 Effective search space: 33670 Effective search space used: 33670 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 (21.6 bits) S2: 45 (21.9 bits)
Align candidate 5209751 Shew_2204 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein (RefSeq))
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.7751.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-34 103.1 1.2 4.9e-34 102.7 0.5 1.5 2 lcl|FitnessBrowser__PV4:5209751 Shew_2204 bifunctional phosphori Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209751 Shew_2204 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophos # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.6 0.0 0.36 0.36 3 14 .. 41 52 .. 40 66 .. 0.72 2 ! 102.7 0.5 4.9e-34 4.9e-34 2 84 .] 115 197 .. 114 197 .. 0.98 Alignments for each domain: == domain 1 score: -2.6 bits; conditional E-value: 0.36 TIGR03188 3 eLeevieerkee 14 +L++++++rk + lcl|FitnessBrowser__PV4:5209751 41 ALAQTLASRKIT 52 688999999865 PP == domain 2 score: 102.7 bits; conditional E-value: 4.9e-34 TIGR03188 2 eeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVllaekgvsled 79 ++L+++i++r+ +d ++Syta+l+e+g+++i++KvgEE E+++aa ++dkeel++Ea+Dl+YhllVll+++++sled lcl|FitnessBrowser__PV4:5209751 115 DNLANLIASRRGQDAKSSYTAHLFERGTKRIAQKVGEEGLETALAAATHDKEELINEASDLIYHLLVLLEDQDLSLED 192 689*************************************************************************** PP TIGR03188 80 vlaeL 84 ++a+L lcl|FitnessBrowser__PV4:5209751 193 ITANL 197 *9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (206 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: 4.57 // [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