Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_078429928.1 BK574_RS20720 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_002019605.1:WP_078429928.1 Length = 208 Score = 178 bits (452), Expect = 5e-50 Identities = 97/205 (47%), Positives = 132/205 (64%), Gaps = 10/205 (4%) Query: 7 RRELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGE 66 + EL +++ GL+P IVQ A S EVL L YMN E+LDKT+E+ + F+SR++Q LW KGE Sbjct: 3 KNELKFDEK-GLIPAIVQDAQSKEVLTLAYMNRESLDKTIETRETWFYSRSRQELWHKGE 61 Query: 67 TSGNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDT---------AHQWLFLYQ 117 TSGN VV + DCD+D L+VL P GP CHKG +CF D+ A ++ + + Sbjct: 62 TSGNTQKVVDLRYDCDSDALVVLVEPSGPACHKGVYTCFADSLLSEEVSTNADRFSIISR 121 Query: 118 LEQLLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLM 177 LE L+AER++ PE SYT L+ G +I +KVGEE E +AA D EL E +DL+ Sbjct: 122 LETLIAEREAEMPEGSYTTYLFDKGVDKILKKVGEEAGEVIIAAKNRDPEELKWEVADLL 181 Query: 178 YHLLVLLQDQGLDLTTVIENLRKRH 202 +HLLVLL++Q L L V+ L +RH Sbjct: 182 FHLLVLLREQKLPLDEVLSVLEERH 206 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: 123 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: 208 Length adjustment: 21 Effective length of query: 182 Effective length of database: 187 Effective search space: 34034 Effective search space used: 34034 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 WP_078429928.1 BK574_RS20720 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE)
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.23226.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-36 110.0 0.6 5e-36 109.1 0.2 1.7 2 lcl|NCBI__GCF_002019605.1:WP_078429928.1 BK574_RS20720 bifunctional phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078429928.1 BK574_RS20720 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.3 0.0 0.28 0.28 3 19 .. 36 52 .. 35 69 .. 0.64 2 ! 109.1 0.2 5e-36 5e-36 2 84 .] 120 202 .. 119 202 .. 0.98 Alignments for each domain: == domain 1 score: -2.3 bits; conditional E-value: 0.28 TIGR03188 3 eLeevieerkeedpeeS 19 +L+++ie r++ + S lcl|NCBI__GCF_002019605.1:WP_078429928.1 36 SLDKTIETRETWFYSRS 52 67888888876544444 PP == domain 2 score: 109.1 bits; conditional E-value: 5e-36 TIGR03188 2 eeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVll 70 ++Le++i+er++e pe+Syt++l++kg dkilkKvgEEa Eviiaakn+d eel +E+aDll+hllVll lcl|NCBI__GCF_002019605.1:WP_078429928.1 120 SRLETLIAEREAEMPEGSYTTYLFDKGVDKILKKVGEEAGEVIIAAKNRDPEELKWEVADLLFHLLVLL 188 79******************************************************************* PP TIGR03188 71 aekgvsledvlaeL 84 +e+ + l++vl++L lcl|NCBI__GCF_002019605.1:WP_078429928.1 189 REQKLPLDEVLSVL 202 **********9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (208 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.68 // [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