Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_028988601.1 G579_RS0100370 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_000423825.1:WP_028988601.1 Length = 235 Score = 155 bits (391), Expect = 7e-43 Identities = 85/202 (42%), Positives = 117/202 (57%), Gaps = 11/202 (5%) Query: 10 LDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSG 69 + W+ GL+P I Q A +GEVLML YM+ E+L TL G T++SR++Q LW KGETSG Sbjct: 14 IKWD-AQGLVPAIAQEARTGEVLMLAYMSRESLAATLRDGYATYYSRSRQSLWRKGETSG 72 Query: 70 NFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCF--GDTAHQW--------LFLYQLE 119 + +V + DCD DTLL+ GP CH G +CF A W L L Sbjct: 73 HLQKLVDLRLDCDGDTLLLRVAQSGPACHTGEDTCFFREQDAGGWSAAAPPPATVLQALC 132 Query: 120 QLLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYH 179 + ++ R+ ADP SY A L+A G +I +KVGEE ET +AA D L E +DL +H Sbjct: 133 ETISARRLADPAQSYVANLFAGGQDKILKKVGEEAAETIIAAKNGDPQALAYETADLFFH 192 Query: 180 LLVLLQDQGLDLTTVIENLRKR 201 +LV+L ++GL + V+ L +R Sbjct: 193 VLVMLVERGLHVNDVLRELARR 214 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: 132 Number of extensions: 8 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: 235 Length adjustment: 22 Effective length of query: 181 Effective length of database: 213 Effective search space: 38553 Effective search space used: 38553 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_028988601.1 G579_RS0100370 (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.17392.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-35 106.1 0.0 6.5e-35 105.5 0.0 1.3 1 lcl|NCBI__GCF_000423825.1:WP_028988601.1 G579_RS0100370 bifunctional phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028988601.1 G579_RS0100370 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosy # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 105.5 0.0 6.5e-35 6.5e-35 1 84 [] 128 211 .. 128 211 .. 0.99 Alignments for each domain: == domain 1 score: 105.5 bits; conditional E-value: 6.5e-35 TIGR03188 1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVl 69 l++L e+i++r+ +dp +Sy+a+l++ g+dkilkKvgEEa+E+iiaakn+d ++l++E+aDl++h+lV+ lcl|NCBI__GCF_000423825.1:WP_028988601.1 128 LQALCETISARRLADPAQSYVANLFAGGQDKILKKVGEEAAETIIAAKNGDPQALAYETADLFFHVLVM 196 7899***************************************************************** PP TIGR03188 70 laekgvsledvlaeL 84 l+e+g++++dvl+eL lcl|NCBI__GCF_000423825.1:WP_028988601.1 197 LVERGLHVNDVLREL 211 *************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (235 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: 6.73 // [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